{"action":"created","comment":{"url":"https://api.github.com/repos/seqan/seqan3/pulls/comments/241795637","pull_request_review_id":185162442,"id":241795637,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDI0MTc5NTYzNw==","diff_hunk":"@@ -35,75 +35,54 @@\n /*!\\file\n  * \\brief Provides global alignment configurations.\n  * \\author Joshua Kim <joshua.kim AT fu-berlin.de>\n+ * \\author Rene Rahn <rene.rahn AT fu-berlin.de>\n  */\n \n #pragma once\n \n-#include <seqan3/alignment/configuration/utility.hpp>\n-#include <seqan3/core/algorithm/all.hpp>\n-#include <seqan3/core/metafunction/basic.hpp>\n-#include <seqan3/core/metafunction/template_inspection.hpp>\n+#include <seqan3/alignment/configuration/detail.hpp>\n+#include <seqan3/core/algorithm/pipeable_config_element.hpp>\n \n namespace seqan3::detail\n {\n-/*!\\brief A configuration element for global alignment.\n- * \\ingroup configuration\n- */\n-struct align_config_global\n+//!\\brief Selects the global alignment mode.\n+//!\\ingroup configuration\n+struct global_alignment_type\n {\n-    //!\\brief The value of align_config_global, true by default.\n-    bool value{true};\n+    //!\\privatesection\n+    //!\\brief An internal id used to check for a valid alignment configuration.\n+    static constexpr detail::align_config_id id{detail::align_config_id::global};\n };\n \n-/*!\\brief The global alignment adaptor enabling pipe notation.\n- * \\ingroup configuration\n- */\n-struct align_config_global_adaptor : public configuration_fn_base<align_config_global_adaptor>\n-{\n-\n-    /*!\\brief Adds to the configuration a global alignment configuration element.\n-     * \\param[in] cfg  The configuration to be extended.\n-     * \\tparam configuration_t The type of the underlying configuration scheme.\n-     *                         Is required to fulfill the seqan3::detail::is_algorithm_configuration requirement.\n-     * \\returns A new configuration containing the global alignment configuration element.\n-     */\n-    template <typename configuration_t>\n-    //!\\cond\n-        requires is_algorithm_configuration_v<remove_cvref_t<configuration_t>>\n-    //!\\endcond\n-    constexpr auto invoke(configuration_t && cfg) const\n-    {\n-        static_assert(is_valid_alignment_configuration_v<align_cfg::id::global, remove_cvref_t<configuration_t>>,\n-                      SEQAN3_INVALID_CONFIG(align_cfg::id::global));\n-\n-        return std::forward<configuration_t>(cfg).push_front(align_config_global{});\n-    }\n-};\n+} // namespace seqan3::detail\n \n-//!\\brief Helper template meta-function associated with seqan3::detail::align_config_global.\n-//!\\ingroup configuration\n-template <>\n-struct on_align_config<align_cfg::id::global>\n+namespace seqan3::align_cfg\n {\n-    //!\\brief Type alias used by meta::find_if\n-    template <config_element_concept t>\n-    using invoke = typename std::is_same<t, align_config_global>::type;\n-};\n \n-//!\\brief Mapping from the seqan3::detail::align_config_global type to its corresponding seqan3::align_cfg::id.\n+//!\\brief Selects global alignment mode.\n //!\\ingroup configuration\n-template <>\n-struct align_config_type_to_id<align_config_global>\n+inline constexpr detail::global_alignment_type global_alignment;","path":"include/seqan3/alignment/configuration/align_config_mode.hpp","position":75,"original_position":75,"commit_id":"fb13c80e24c48d982970e0c4e044d89c9b4bdac8","original_commit_id":"fb13c80e24c48d982970e0c4e044d89c9b4bdac8","user":{"login":"rrahn","id":1529364,"node_id":"MDQ6VXNlcjE1MjkzNjQ=","avatar_url":"https://avatars2.githubusercontent.com/u/1529364?v=4","gravatar_id":"","url":"https://api.github.com/users/rrahn","html_url":"https://github.com/rrahn","followers_url":"https://api.github.com/users/rrahn/followers","following_url":"https://api.github.com/users/rrahn/following{/other_user}","gists_url":"https://api.github.com/users/rrahn/gists{/gist_id}","starred_url":"https://api.github.com/users/rrahn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rrahn/subscriptions","organizations_url":"https://api.github.com/users/rrahn/orgs","repos_url":"https://api.github.com/users/rrahn/repos","events_url":"https://api.github.com/users/rrahn/events{/privacy}","received_events_url":"https://api.github.com/users/rrahn/received_events","type":"User","site_admin":false},"body":"No, it is currently not implemented. These things will be added iteratively.","created_at":"2018-12-14T15:39:59Z","updated_at":"2018-12-14T15:39:59Z","html_url":"https://github.com/seqan/seqan3/pull/567#discussion_r241795637","pull_request_url":"https://api.github.com/repos/seqan/seqan3/pulls/567","author_association":"COLLABORATOR","_links":{"self":{"href":"https://api.github.com/repos/seqan/seqan3/pulls/comments/241795637"},"html":{"href":"https://github.com/seqan/seqan3/pull/567#discussion_r241795637"},"pull_request":{"href":"https://api.github.com/repos/seqan/seqan3/pulls/567"}},"in_reply_to_id":241758470},"pull_request":{"url":"https://api.github.com/repos/seqan/seqan3/pulls/567","id":231663478,"node_id":"MDExOlB1bGxSZXF1ZXN0MjMxNjYzNDc4","html_url":"https://github.com/seqan/seqan3/pull/567","diff_url":"https://github.com/seqan/seqan3/pull/567.diff","patch_url":"https://github.com/seqan/seqan3/pull/567.patch","issue_url":"https://api.github.com/repos/seqan/seqan3/issues/567","number":567,"state":"open","locked":false,"title":"Feature/rework configuration","user":{"login":"rrahn","id":1529364,"node_id":"MDQ6VXNlcjE1MjkzNjQ=","avatar_url":"https://avatars2.githubusercontent.com/u/1529364?v=4","gravatar_id":"","url":"https://api.github.com/users/rrahn","html_url":"https://github.com/rrahn","followers_url":"https://api.github.com/users/rrahn/followers","following_url":"https://api.github.com/users/rrahn/following{/other_user}","gists_url":"https://api.github.com/users/rrahn/gists{/gist_id}","starred_url":"https://api.github.com/users/rrahn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rrahn/subscriptions","organizations_url":"https://api.github.com/users/rrahn/orgs","repos_url":"https://api.github.com/users/rrahn/repos","events_url":"https://api.github.com/users/rrahn/events{/privacy}","received_events_url":"https://api.github.com/users/rrahn/received_events","type":"User","site_admin":false},"body":"Major rework of the configuration system to reduce a lot of boiler plate code and maintain a more leightweight code basis.\r\nMakes querying the configuration more intutive.\r\nAlso it will make it a whole lot aeasier to document the configurations for algorithms.\r\n\r\nThis is still WIP, but I want to share it early, as it will change a lot of the exisiting configurations.\r\n\r\n### Blocked\r\n* <s>#566</s>\r\n* ~#370~\r\n* ~#613~\r\n\r\n###  TODO\r\n* [x] Adapt existing alignment configurations\r\n* [x] Adapt existing search configurations\r\n* [x] reevaluate the replace_with function\r\n* [x] reevaluate the deferred_config (maybe this is better done within the implementation of the algorithm.)\r\n* [x] remove some unused code in configuration\r\n* [x] check if all new files have a short header.\r\n* [x] make some more types aggregate\r\n* [x] Check commented block in test\r\n* [x] Revert changes in scoring scheme implementation\r\n* [x] make gap scheme concept work with score function only.\r\n* [x] double view::persist in align_pairwise\r\n* [x] Remove is_algorithm_configuration unary type trait.\r\n* [x] rename the aligned_ends using `first` and `second` prefix\r\n\r\n### State\r\n\r\nExcept for some smaller things like fixing doxygen or removing unused code this is in a final state.\r\nI suggest going through commit by commit as they are separated per configuration element and some basic units. Also please note, that the docu will for this PR only cover very basic coverage. For the upcoming sprints I plan to make the documentation more verbose, but it depends on other stuff too.","created_at":"2018-11-16T21:42:23Z","updated_at":"2018-12-14T15:39:59Z","closed_at":null,"merged_at":null,"merge_commit_sha":"dd46a50b78dc85a47dc9be2031c07fdd852b6ea9","assignee":{"login":"h-2","id":2996863,"node_id":"MDQ6VXNlcjI5OTY4NjM=","avatar_url":"https://avatars2.githubusercontent.com/u/2996863?v=4","gravatar_id":"","url":"https://api.github.com/users/h-2","html_url":"https://github.com/h-2","followers_url":"https://api.github.com/users/h-2/followers","following_url":"https://api.github.com/users/h-2/following{/other_user}","gists_url":"https://api.github.com/users/h-2/gists{/gist_id}","starred_url":"https://api.github.com/users/h-2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/h-2/subscriptions","organizations_url":"https://api.github.com/users/h-2/orgs","repos_url":"https://api.github.com/users/h-2/repos","events_url":"https://api.github.com/users/h-2/events{/privacy}","received_events_url":"https://api.github.com/users/h-2/received_events","type":"User","site_admin":false},"assignees":[{"login":"h-2","id":2996863,"node_id":"MDQ6VXNlcjI5OTY4NjM=","avatar_url":"https://avatars2.githubusercontent.com/u/2996863?v=4","gravatar_id":"","url":"https://api.github.com/users/h-2","html_url":"https://github.com/h-2","followers_url":"https://api.github.com/users/h-2/followers","following_url":"https://api.github.com/users/h-2/following{/other_user}","gists_url":"https://api.github.com/users/h-2/gists{/gist_id}","starred_url":"https://api.github.com/users/h-2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/h-2/subscriptions","organizations_url":"https://api.github.com/users/h-2/orgs","repos_url":"https://api.github.com/users/h-2/repos","events_url":"https://api.github.com/users/h-2/events{/privacy}","received_events_url":"https://api.github.com/users/h-2/received_events","type":"User","site_admin":false}],"requested_reviewers":[{"login":"h-2","id":2996863,"node_id":"MDQ6VXNlcjI5OTY4NjM=","avatar_url":"https://avatars2.githubusercontent.com/u/2996863?v=4","gravatar_id":"","url":"https://api.github.com/users/h-2","html_url":"https://github.com/h-2","followers_url":"https://api.github.com/users/h-2/followers","following_url":"https://api.github.com/users/h-2/following{/other_user}","gists_url":"https://api.github.com/users/h-2/gists{/gist_id}","starred_url":"https://api.github.com/users/h-2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/h-2/subscriptions","organizations_url":"https://api.github.com/users/h-2/orgs","repos_url":"https://api.github.com/users/h-2/repos","events_url":"https://api.github.com/users/h-2/events{/privacy}","received_events_url":"https://api.github.com/users/h-2/received_events","type":"User","site_admin":false}],"requested_teams":[],"labels":[],"milestone":{"url":"https://api.github.com/repos/seqan/seqan3/milestones/12","html_url":"https://github.com/seqan/seqan3/milestone/12","labels_url":"https://api.github.com/repos/seqan/seqan3/milestones/12/labels","id":3833107,"node_id":"MDk6TWlsZXN0b25lMzgzMzEwNw==","number":12,"title":"December 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