[FEATURE] Make search modi into individual pipeable config elements.

CHANGELOG.md

@@ -72,6 +72,13 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
 #### Search
 
 * Moved `seqan3::search` from `search/algorithm/` to `search/` ([\#1696](https://github.com/seqan/seqan3/pull/1696)).
+* Configuration refactoring:
+  * The names for the search mode configuration have changed and are now individual config elements
+    that are pipeable ([\#1639](https://github.com/seqan/seqan3/pull/1639)):
+    `seqan3::search_cfg::all` to `seqan3::search_cfg::hit_all`
+    `seqan3::search_cfg::best` to `seqan3::search_cfg::hit_single_best`
+    `seqan3::search_cfg::all_best` to `seqan3::search_cfg::hit_all_best`
+    `seqan3::search_cfg::strata{5}` to `seqan3::search_cfg::hit_strata{5}`
 
 ## Notable Bug-fixes
 

doc/tutorial/read_mapper/read_mapper_step2.cpp

@@ -48,7 +48,7 @@ void map_reads(std::filesystem::path const & query_path,
     seqan3::sequence_file_input query_in{query_path};
 
     seqan3::configuration const search_config = seqan3::search_cfg::max_error{seqan3::search_cfg::total{errors}} |
-                                                seqan3::search_cfg::mode{seqan3::search_cfg::all_best};
+                                                seqan3::search_cfg::hit_all_best;
 
     for (auto & [query, id, qual] : query_in | seqan3::views::take(20))
     {

doc/tutorial/read_mapper/read_mapper_step3.cpp

@@ -49,7 +49,7 @@ void map_reads(std::filesystem::path const & query_path,
     seqan3::sequence_file_input query_in{query_path};
 
     seqan3::configuration const search_config = seqan3::search_cfg::max_error{seqan3::search_cfg::total{errors}} |
-                                                seqan3::search_cfg::mode{seqan3::search_cfg::all_best};
+                                                seqan3::search_cfg::hit_all_best;
 
 //! [alignment_config]
     seqan3::configuration const align_config = seqan3::align_cfg::edit |

doc/tutorial/read_mapper/read_mapper_step4.cpp

@@ -59,7 +59,7 @@ void map_reads(std::filesystem::path const & query_path,
 //! [alignment_file_output]
 
     seqan3::configuration const search_config = seqan3::search_cfg::max_error{seqan3::search_cfg::total{errors}} |
-                                                seqan3::search_cfg::mode{seqan3::search_cfg::all_best};
+                                                seqan3::search_cfg::hit_all_best;
 
     seqan3::configuration const align_config = seqan3::align_cfg::edit |
                                                seqan3::align_cfg::aligned_ends{seqan3::free_ends_first} |

doc/tutorial/search/index.md

@@ -216,10 +216,10 @@ At position 85: ACT
 
 Besides the error configuration, you can define what kind of hits should be reported:
 
-- seqan3::search_cfg::all: Report all hits that satisfy the (approximate) search.
-- seqan3::search_cfg::best: Report the best hit, i.e. the *first* hit with the lowest edit distance.
-- seqan3::search_cfg::all_best: Report all hits with the lowest edit distance.
-- seqan3::search_cfg::strata: best+x mode. Report all hits within the x-neighbourhood of the best hit.
+- seqan3::search_cfg::hit_all: Report all hits that satisfy the (approximate) search.
+- seqan3::search_cfg::hit_single_best: Report the best hit, i.e. the *first* hit with the lowest edit distance.
+- seqan3::search_cfg::hit_all_best: Report all hits with the lowest edit distance.
+- seqan3::search_cfg::hit_strata: best+x mode. Report all hits within the x-neighbourhood of the best hit.
 
 The mode is appended to the error configuration by using the `|`-operator:
 \snippet doc/tutorial/search/search_small_snippets.cpp mode_best

doc/tutorial/search/search_small_snippets.cpp

@@ -94,7 +94,7 @@ seqan3::configuration const cfg = seqan3::search_cfg::max_error{seqan3::search_c
                                                                 seqan3::search_cfg::substitution{0},
                                                                 seqan3::search_cfg::insertion{1},
                                                                 seqan3::search_cfg::deletion{1}} |
-                                                                seqan3::search_cfg::mode{seqan3::search_cfg::best};
+                                  seqan3::search_cfg::hit_single_best;
 //![mode_best]
 }
 
@@ -104,7 +104,7 @@ seqan3::configuration const cfg = seqan3::search_cfg::max_error{seqan3::search_c
                                                                 seqan3::search_cfg::substitution{0},
                                                                 seqan3::search_cfg::insertion{1},
                                                                 seqan3::search_cfg::deletion{1}} |
-                                                                seqan3::search_cfg::mode{seqan3::search_cfg::strata{2}};
+                                  seqan3::search_cfg::hit_strata{2};
 //![mode_strata]
 }
 

doc/tutorial/search/search_solution4.cpp

@@ -15,25 +15,25 @@ int main()
 
     seqan3::debug_stream << "Searching all hits\n";
     seqan3::configuration const cfg_all = seqan3::search_cfg::max_error{seqan3::search_cfg::total{1}} |
-                                          seqan3::search_cfg::mode{seqan3::search_cfg::all};
+                                          seqan3::search_cfg::hit_all;
     auto results_all = search(query, index, cfg_all);
     seqan3::debug_stream << "Hits: " << results_all << "\n";
 
     seqan3::debug_stream << "Searching all best hits\n";
     seqan3::configuration const cfg_all_best = seqan3::search_cfg::max_error{seqan3::search_cfg::total{1}} |
-                                               seqan3::search_cfg::mode{seqan3::search_cfg::all_best};
+                                               seqan3::search_cfg::hit_all_best;
     auto results_all_best = search(query, index, cfg_all_best);
     seqan3::debug_stream << "Hits: " << results_all_best << "\n";
 
     seqan3::debug_stream << "Searching best hit\n";
     seqan3::configuration const cfg_best = seqan3::search_cfg::max_error{seqan3::search_cfg::total{1}} |
-                                           seqan3::search_cfg::mode{seqan3::search_cfg::best};
+                                           seqan3::search_cfg::hit_single_best;
     auto results_best = search(query, index, cfg_best);
     seqan3::debug_stream << "Hits " << results_best << "\n";
 
     seqan3::debug_stream << "Searching all hits in the 1-stratum\n";
     seqan3::configuration const cfg_strata = seqan3::search_cfg::max_error{seqan3::search_cfg::total{1}} |
-                                             seqan3::search_cfg::mode{seqan3::search_cfg::strata{1}};
+                                             seqan3::search_cfg::hit_strata{1};
     auto results_strata = search(query, index, cfg_strata);
     seqan3::debug_stream << "Hits: " << results_strata << "\n";
 }

doc/tutorial/search/search_solution5.cpp

@@ -18,7 +18,7 @@ void run_text_single()
     seqan3::debug_stream << "Searching all best hits allowing for 1 error in a single text\n";
 
     seqan3::configuration const search_config = seqan3::search_cfg::max_error{seqan3::search_cfg::total{1}} |
-                                                seqan3::search_cfg::mode{seqan3::search_cfg::all_best};
+                                                seqan3::search_cfg::hit_all_best;
     seqan3::configuration const align_config = seqan3::align_cfg::edit |
                                                seqan3::align_cfg::aligned_ends{seqan3::free_ends_first} |
                                                seqan3::align_cfg::result{seqan3::with_alignment};
@@ -54,7 +54,7 @@ void run_text_collection()
     seqan3::debug_stream << "Searching all best hits allowing for 1 error in a text collection\n";
 
     seqan3::configuration const search_config = seqan3::search_cfg::max_error{seqan3::search_cfg::total{1}} |
-                                                seqan3::search_cfg::mode{seqan3::search_cfg::all_best};
+                                                seqan3::search_cfg::hit_all_best;
     seqan3::configuration const align_config = seqan3::align_cfg::edit |
                                                seqan3::align_cfg::aligned_ends{seqan3::free_ends_first} |
                                                seqan3::align_cfg::result{seqan3::with_alignment};

include/seqan3/search/configuration/default_configuration.hpp

@@ -27,6 +27,6 @@ namespace seqan3::search_cfg
  */
 inline constexpr configuration default_configuration = max_error{total{0}, substitution{0}, insertion{0}, deletion{0}} |
                                                        output{text_position} |
-                                                       mode{all};
+                                                       hit_all;
 
 } // namespace seqan3::search_cfg

include/seqan3/search/configuration/mode.hpp

@@ -6,97 +6,109 @@
 // -----------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Provides the mode configuration to define the search modes "all", "all_best", "best" and "strata".
+ * \brief Provides the mode configuration to define the search modes "hit_strata", "hit_all",
+ *        "hit_all_best", "hit_single_best".
  * \author Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>
  * \author Rene Rahn <rene.rahn AT fu-berlin.de>
+ * \author Svenja Mehringer <svenja.mehringer AT fu-berlin.de>
  */
 
 #pragma once
 
-#include <seqan3/core/algorithm/configuration.hpp>
+#include <variant>
+
 #include <seqan3/core/algorithm/pipeable_config_element.hpp>
-#include <seqan3/core/detail/strong_type.hpp>
-#include <seqan3/core/type_traits/basic.hpp>
+#include <seqan3/core/detail/empty_type.hpp>
+#include <seqan3/core/detail/test_accessor.hpp>
+#include <seqan3/core/type_list/traits.hpp>
+#include <seqan3/core/type_traits/template_inspection.hpp>
 #include <seqan3/search/configuration/detail.hpp>
 
-
 namespace seqan3::detail
 {
 
-//!\brief Type for the "all" value for the configuration element "mode".
-//!\ingroup search_configuration
-struct search_mode_all {};
-//!\brief Type for the "all_best" value for the configuration element "mode".
-//!\ingroup search_configuration
-struct search_mode_all_best {};
-//!\brief Type for the "best" value for the configuration element "mode".
-//!\ingroup search_configuration
-struct search_mode_best {};
-
-} // namespace seqan3::detail
-
-namespace seqan3::search_cfg
+/*!\brief Configuration element to receive all hits within the error bounds.
+ * \ingroup search_configuration
+ */
+struct hit_all_tag : public pipeable_config_element<hit_all_tag, empty_type>
 {
+    //!\privatesection
+    //!\brief Internal id to check for consistent configuration settings.
+    static constexpr detail::search_config_id id{detail::search_config_id::mode};
+};
 
-//!\brief Configuration element to receive all hits within the error bounds.
-//!\ingroup search_configuration
-inline detail::search_mode_all constexpr all;
-//!\brief Configuration element to receive all hits within the lowest number of errors.
-//!\ingroup search_configuration
-inline detail::search_mode_all_best constexpr all_best;
-//!\brief Configuration element to receive one best hit (with the lowest number of errors).
-//!\ingroup search_configuration
-inline detail::search_mode_best constexpr best;
-
-/*!\brief Configuration element to receive all hits with the best number of errors plus the strata value.
- *        A strong type of underlying type `uint8_t` that represents the number or errors for strata.
- *        All hits are found with the fewest number of errors plus 'value'.
+/*!\brief Configuration element to receive all hits with the lowest number of errors within the bounds
  * \ingroup search_configuration
- * \tparam value_t The underlying type.
  */
-struct strata : detail::strong_type<uint8_t, strata, detail::strong_type_skill::convert>
+struct hit_all_best_tag : public pipeable_config_element<hit_all_best_tag, empty_type>
 {
-    using detail::strong_type<uint8_t, strata, detail::strong_type_skill::convert>::strong_type;
+    //!\privatesection
+    //!\brief Internal id to check for consistent configuration settings.
+    static constexpr detail::search_config_id id{detail::search_config_id::mode};
 };
 
 /*!\brief Configuration element to determine the search mode.
  * \ingroup search_configuration
- *
+ */
+struct hit_single_best_tag : public pipeable_config_element<hit_single_best_tag, empty_type>
+{
+    //!\privatesection
+    //!\brief Internal id to check for consistent configuration settings.
+    static constexpr detail::search_config_id id{detail::search_config_id::mode};
+};
+
+} // namespace seqan3::detail
+
+namespace seqan3::search_cfg
+{
+
+/*!\brief Configuration element to receive all hits within the error bounds.
+ * \ingroup search_configuration
  * \details
  * This configuration element can be used to determine which hits are supported.
  * Currently these modes are available:
- * | Mode                         | Behaviour                                                           |
- * |------------------------------|---------------------------------------------------------------------|
- * | seqan3::search_cfg::all      | Report all hits within error bounds.                                |
- * | seqan3::search_cfg::all_best | Report all hits with the lowest number of errors within the bounds. |
- * | seqan3::search_cfg::best     | Report one best hit (hit with lowest error) within bounds.          |
- * | seqan3::search_cfg::strata   | Report all hits within best + x errors.                             |
+ *
+ * | Mode                                        | Behaviour                                                           |
+ * |---------------------------------------------|---------------------------------------------------------------------|
+ * | seqan3::search_cfg::hit_all         | Report all hits within error bounds.                                |
+ * | seqan3::search_cfg::hit_all_best    | Report all hits with the lowest number of errors within the bounds. |
+ * | seqan3::search_cfg::hit_single_best | Report one best hit (hit with lowest error) within bounds.          |
+ * | seqan3::search_cfg::hit_strata      | Report all hits within best + x errors.                             |
+ *
+ * The individual configuration elements to select a search mode cannot be combined with each other.
  *
  * ### Example
  *
  * \include test/snippet/search/configuration_modes.cpp
+ *
+ * \hideinitializer
  */
-template <typename mode_t>
-//!\cond
-    requires std::same_as<remove_cvref_t<mode_t>, detail::search_mode_all> ||
-             std::same_as<remove_cvref_t<mode_t>, detail::search_mode_all_best> ||
-             std::same_as<remove_cvref_t<mode_t>, detail::search_mode_best> ||
-             std::same_as<remove_cvref_t<mode_t>, strata>
-//!\endcond
-struct mode : public pipeable_config_element<mode<mode_t>, mode_t>
+inline constexpr detail::hit_all_tag hit_all{};
+
+/*!\brief Configuration element to receive all hits with the lowest number of errors within the bounds.
+ * \ingroup search_configuration
+ * \copydetails seqan3::search_cfg::hit_all
+ * \hideinitializer
+ */
+inline constexpr detail::hit_all_best_tag hit_all_best{};
+
+/*!\brief Configuration element to receive one best hit (with the lowest number of errors).
+ * \ingroup search_configuration
+ * \copydetails seqan3::search_cfg::hit_all
+ * \hideinitializer
+ */
+inline constexpr detail::hit_single_best_tag hit_single_best{};
+
+/*!\brief Configuration element to receive all hits with the best number of errors plus the strata value.
+ *        All hits are found with the fewest number of errors plus 'stratum'.
+ * \ingroup search_configuration
+ * \copydetails seqan3::search_cfg::hit_all
+ */
+struct hit_strata : public pipeable_config_element<hit_strata, uint8_t>
 {
     //!\privatesection
     //!\brief Internal id to check for consistent configuration settings.
     static constexpr detail::search_config_id id{detail::search_config_id::mode};
 };
 
-/*!\name Type deduction guides
- * \relates seqan3::search_cfg::mode
- * \{
- */
-
-//!\brief Deduces search mode type from constructor argument.
-template <typename mode_t>
-mode(mode_t) -> mode<remove_cvref_t<mode_t>>;
-//!\}
 } // namespace seqan3::search_cfg

include/seqan3/search/detail/search_scheme_algorithm.hpp

@@ -133,7 +133,7 @@ class search_scheme_algorithm : protected policies_t...
                 if (!internal_hits.empty())
                 {
                     internal_hits.clear(); // TODO:don't clear when using Optimum Search Schemes with lower error bounds
-                    uint8_t const stratum = get<search_cfg::mode>(config).value;
+                    uint8_t const stratum = get<search_cfg::hit_strata>(config).value;
                     error_state.total += stratum - 1;
                     search_algo_bi<false>(query, error_state, on_hit_delegate);
                 }

include/seqan3/search/detail/search_traits.hpp

@@ -42,17 +42,13 @@ struct search_traits
     static constexpr bool has_error_configuration = search_with_max_error | search_with_max_error_rate;
 
     //!\brief A flag indicating whether search should find all hits.
-    static constexpr bool search_all_hits =
-        search_configuration_t::template exists<search_cfg::mode<detail::search_mode_all>>();
+    static constexpr bool search_all_hits = search_configuration_t::template exists<hit_all_tag>();
     //!\brief A flag indicating whether search should find best hits.
-    static constexpr bool search_best_hits =
-        search_configuration_t::template exists<search_cfg::mode<detail::search_mode_best>>();
+    static constexpr bool search_best_hits = search_configuration_t::template exists<hit_single_best_tag>();
     //!\brief A flag indicating whether search should find all best hits.
-    static constexpr bool search_all_best_hits =
-        search_configuration_t::template exists<search_cfg::mode<detail::search_mode_all_best>>();
+    static constexpr bool search_all_best_hits = search_configuration_t::template exists<hit_all_best_tag>();
     //!\brief A flag indicating whether search should find strata hits.
-    static constexpr bool search_strata_hits =
-        search_configuration_t::template exists<search_cfg::mode<search_cfg::strata>>();
+    static constexpr bool search_strata_hits = search_configuration_t::template exists<search_cfg::hit_strata>();
     //!\brief A flag indicating whether mode configuration was set in the search configuration.
     static constexpr bool has_mode_configuration = search_all_hits |
                                                    search_best_hits |

include/seqan3/search/detail/unidirectional_search_algorithm.hpp

@@ -152,7 +152,7 @@ class unidirectional_search_algorithm : protected policies_t...
                 if (!internal_hits.empty())
                 {
                     internal_hits.clear();
-                    uint8_t const stratum = get<search_cfg::mode>(config).value;
+                    uint8_t const stratum = get<search_cfg::hit_strata>(config).value;
                     error_state.total += stratum - 1;
                     search_trivial<false>(index_ptr->cursor(), query, 0, error_state, error_type::none);
                 }

include/seqan3/search/search.hpp

@@ -34,20 +34,20 @@ namespace seqan3::detail
  */
 struct search_configurator
 {
-    /*!\brief Add seqan3::search_cfg::all to the configuration if seqan3::search_cfg::mode was not set.
+    /*!\brief Add seqan3::search_cfg::hit_all to the configuration if seqan3::search_cfg::mode was not set.
      * \tparam configuration_t The type of the search configuration.
      * \param[in] cfg The configuration to be modified if necessary.
      * \returns The configuration which is guaranteed to have a seqan3::search_cfg::mode available.
      *
      * \details
      *
-     * If seqan3::search_cfg::mode was not set, it defaults to seqan3::search_cfg::all.
+     * If seqan3::search_cfg::mode was not set, it defaults to seqan3::search_cfg::hit_all.
      */
     template <typename configuration_t>
     static auto add_default_mode_configuration(configuration_t const & cfg)
     {
         if constexpr (!detail::search_traits<configuration_t>::has_mode_configuration)
-            return cfg | search_cfg::mode{search_cfg::all};
+            return cfg | search_cfg::hit_all;
         else
             return cfg;
     }