[MISC] Add alphabet type template to fm_index

CHANGELOG.md

@@ -40,6 +40,15 @@ If possible, provide tooling that performs the changes, e.g. a shell-script.
 * **The `type_list` header has moved:**
   If you included `<seqan3/core/type_list.hpp>` you need to change the path to `<seqan3/core/type_list/type_list.hpp>`.
 
+#### Search
+
+* **Changed class signature of (bi_)fm_index:**
+  All code that relies on automatic template deduction will be unaffected. In case you specified the template parameters
+  of an `seqan3::fm_index` or `seqan3::bi_fm_index` you will need to add the alphabet type as first parameter and pass a
+  `seqan3::text_layout` instead of a `bool` to indicate the text layout (single, collection).
+  For example, `fm_index<false> index{text}` where `text` is of type `dna4_vector` needs to be changed to
+  `fm_index<dna4, text_layout::single> index{text}`.
+
 ## Notable Bug-fixes
 
 # 3.0.0 ("Escala")

doc/tutorial/read_mapper/read_mapper_step2.cpp

@@ -38,7 +38,7 @@ void map_reads(std::filesystem::path const & query_path,
                uint8_t const errors)
 //! [map_reads]
 {
-    bi_fm_index<text_layout::collection> index; // we need to know if we work on a text collection before loading
+    bi_fm_index<dna5, text_layout::collection> index; // we need to the alphabet and text layout before loading
     {
         std::ifstream is{index_path, std::ios::binary};
         cereal::BinaryInputArchive iarchive{is};

doc/tutorial/read_mapper/read_mapper_step3.cpp

@@ -39,7 +39,7 @@ void map_reads(std::filesystem::path const & query_path,
                reference_storage_t & storage,
                uint8_t const errors)
 {
-    bi_fm_index<text_layout::collection> index; // we need to know if we work on a text collection before loading
+    bi_fm_index<dna5, text_layout::collection> index; // we need to the alphabet and text layout before loading
     {
         std::ifstream is{index_path, std::ios::binary};
         cereal::BinaryInputArchive iarchive{is};

doc/tutorial/read_mapper/read_mapper_step4.cpp

@@ -40,7 +40,7 @@ void map_reads(std::filesystem::path const & query_path,
                reference_storage_t & storage,
                uint8_t const errors)
 {
-    bi_fm_index<text_layout::collection> index; // we need to know if we work on a text collection before loading
+    bi_fm_index<dna5, text_layout::collection> index; // we need to the alphabet and text layout before loading
     {
         std::ifstream is{index_path, std::ios::binary};
         cereal::BinaryInputArchive iarchive{is};

doc/tutorial/search/search_small_snippets.cpp

@@ -48,7 +48,8 @@ fm_index index{text};
 
 {
 //![load]
-fm_index<text_layout::single> index; // we need to tell the index that we work on a single text before loading
+// we need to tell the index that we work on a single text and a `char` alphabet before loading
+fm_index<char, text_layout::single> index;
 {
     std::ifstream is{"index.file", std::ios::binary};
     cereal::BinaryInputArchive iarchive{is};

doc/tutorial/search/search_solution1.cpp

@@ -23,7 +23,8 @@ int main()
         oarchive(index);
     }
 
-    fm_index<text_layout::single> index2; // we need to tell the index that we work on a single text before loading
+    // we need to tell the index that we work on a single text and a `dna4` alphabet before loading
+    fm_index<dna4, text_layout::single> index2;
     {
         std::ifstream is{"index.file", std::ios::binary};
         cereal::BinaryInputArchive iarchive{is};

include/seqan3/search/algorithm/detail/search.hpp

@@ -130,7 +130,7 @@ inline auto search_single(index_t const & index, query_t & query, configuration_
     }
     else
     {
-        using hit_t = std::conditional_t<index_t::is_collection_,
+        using hit_t = std::conditional_t<index_t::is_collection,
                                          std::pair<typename index_t::size_type, typename index_t::size_type>,
                                          typename index_t::size_type>;
         std::vector<hit_t> hits;
@@ -184,7 +184,7 @@ inline auto search_all(index_t const & index, queries_t & queries, configuration
     // delegate params: text_position (or cursor). we will withhold all hits of one query anyway to filter
     //                  duplicates. more efficient to call delegate once with one vector instead of calling
     //                  delegate for each hit separately at once.
-    using text_pos_t = std::conditional_t<index_t::is_collection_,
+    using text_pos_t = std::conditional_t<index_t::is_collection,
                                           std::pair<typename index_t::size_type, typename index_t::size_type>,
                                           typename index_t::size_type>;
     using hit_t = std::conditional_t<cfg_t::template exists<search_cfg::output<detail::search_output_index_cursor>>(),

include/seqan3/search/algorithm/detail/search_trivial.hpp

@@ -15,6 +15,7 @@
 
 #include <type_traits>
 
+#include <seqan3/alphabet/concept.hpp>
 #include <seqan3/range/concept.hpp>
 #include <seqan3/range/view/drop.hpp>
 #include <seqan3/search/algorithm/detail/search_common.hpp>

include/seqan3/search/fm_index/bi_fm_index.hpp

@@ -24,22 +24,13 @@
 namespace seqan3
 {
 
-//!\cond
-SEQAN3_DEPRECATED_310
-void bi_fm_index_deprecation(bool);
-
-template <typename t>
-void bi_fm_index_deprecation(t);
-//!\endcond
-
 /*!\addtogroup submodule_fm_index
  * \{
  */
 
 /*!\brief The SeqAn Bidirectional FM Index
  * \implements seqan3::BiFmIndex
- * \tparam is_collection    Indicates whether this index works on a text collection or a single text.
- *                          See seqan3::text_layout.
+ * \tparam text_t           The type the underlying text range; must model std::ranges::BidirectionalRange.
  * \tparam sdsl_index_type_ The type of the underlying SDSL index, must model seqan3::SdslIndex.
  * \details
  *
@@ -64,18 +55,13 @@ void bi_fm_index_deprecation(t);
  *
  * \attention When building an index for a **text collection** over any alphabet, the symbols with rank 254 and 255
  *            are reserved and may not be used in the text.
- *
- * \deprecated Use seqan3::text_layout to indicate single texts and text collections. The use of bool is deprecated.
  */
-template <auto is_collection = text_layout::single, detail::SdslIndex sdsl_index_type_ = default_sdsl_index_type>
+template <Semialphabet alphabet_t,
+          text_layout text_layout_mode,
+          detail::SdslIndex sdsl_index_type_ = default_sdsl_index_type>
 class bi_fm_index
 {
 protected:
-    //!\brief The alphabet size of the text.
-    size_t sigma{0};
-    //!\brief Indicates whether index is built over a collection.
-    static constexpr bool is_collection_{is_collection};
-
     /*!\name Index types
      * \{
      */
@@ -93,27 +79,22 @@ class bi_fm_index
     //!\brief The type of the alphabet size of the underlying SDSL index.
     using sdsl_sigma_type = typename sdsl_index_type::alphabet_type::sigma_type;
 
-    //!\brief The type of the underlying FM index for the original text.
-    using fm_index_type = fm_index<text_layout{is_collection_}, sdsl_index_type>;
-
-    //!\brief The type of the underlying FM index for the reversed text.\if DEV \todo Change sampling behaviour. \endif
-    using rev_fm_index_type = fm_index<text_layout{is_collection_}, sdsl_index_type>;
+    //!\brief The type of the underlying FM index.
+    using fm_index_type = fm_index<alphabet_t, text_layout_mode, sdsl_index_type>;
     //!\}
 
     //!\brief Underlying FM index for the original text.
     fm_index_type fwd_fm;
 
     //!\brief Underlying FM index for the reversed text.
-    rev_fm_index_type rev_fm;
-
-    //!\cond
-    using unused_t [[maybe_unused]] = decltype(bi_fm_index_deprecation(is_collection));
-    //!\endcond
+    fm_index_type rev_fm;
 
 public:
     /*!\name Text types
      * \{
      */
+    //!\brief The type of the underlying character of the indexed text.
+    using char_type = typename fm_index_type::char_type;
     //!\brief Type for representing positions in the indexed text.
     using size_type = typename sdsl_index_type::size_type;
     //!\}
@@ -122,13 +103,14 @@ class bi_fm_index
      * \{
      */
     //!\brief The type of the bidirectional cursor.
-    using cursor_type = bi_fm_index_cursor<bi_fm_index<is_collection, sdsl_index_type>>;
-    //!\brief The type of the unidirectional cursor on the original text.
-    using fwd_cursor_type = fm_index_cursor<fm_index_type>;
-    //!\brief The type of the unidirectional cursor on the reversed text.
-    using rev_cursor_type = fm_index_cursor<rev_fm_index_type>;
+    using cursor_type = bi_fm_index_cursor<bi_fm_index<alphabet_t, text_layout_mode, sdsl_index_type>>;
+    //!\brief The type of the unidirectional cursor.
+    using uni_cursor_type = fm_index_cursor<fm_index_type>;
     //!\}
 
+    //!\brief Indicates whether index is built over a collection.
+    static constexpr bool is_collection = text_layout_mode;
+
     template <typename fm_index_t>
     friend class fm_index_cursor;
 
@@ -153,7 +135,7 @@ class bi_fm_index
     template <std::ranges::Range text_t>
     bi_fm_index(text_t && text)
     {
-        construct(std::forward<decltype(text)>(text));
+        construct(std::forward<text_t>(text));
     }
     //!\}
 
@@ -177,9 +159,9 @@ class bi_fm_index
      * No guarantee. \if DEV \todo Ensure strong exception guarantee. \endif
      */
     template <std::ranges::Range text_t>
-        //!\cond
-    requires !is_collection_
-        //!\endcond
+    //!\cond
+        requires !is_collection
+    //!\endcond
     void construct(text_t && text)
     {
         static_assert(std::ranges::BidirectionalRange<text_t>, "The text must model BidirectionalRange.");
@@ -193,15 +175,13 @@ class bi_fm_index
         auto rev_text = std::view::reverse(text);
         fwd_fm.construct(text);
         rev_fm.construct(rev_text);
-
-        sigma = fwd_fm.sigma;
     }
 
     //!\overload
     template <std::ranges::Range text_t>
-        //!\cond
-        requires is_collection_
-        //!\endcond
+    //!\cond
+        requires is_collection
+    //!\endcond
     void construct(text_t && text)
     {
         static_assert(std::ranges::BidirectionalRange<text_t>, "The text must model BidirectionalRange.");
@@ -217,8 +197,6 @@ class bi_fm_index
         auto rev_text = text | view::deep{std::view::reverse} | std::view::reverse;
         fwd_fm.construct(text);
         rev_fm.construct(rev_text);
-
-        sigma = fwd_fm.sigma;
     }
 
     /*!\brief Returns the length of the indexed text including sentinel characters.
@@ -316,7 +294,7 @@ class bi_fm_index
      *
      * No-throw guarantee.
      */
-    fwd_cursor_type fwd_begin() const noexcept
+    uni_cursor_type fwd_begin() const noexcept
     {
        return {fwd_fm};
     }
@@ -335,7 +313,7 @@ class bi_fm_index
      *
      * No-throw guarantee.
      */
-    rev_cursor_type rev_begin() const noexcept
+    uni_cursor_type rev_begin() const noexcept
     {
        return {rev_fm};
     }
@@ -361,7 +339,7 @@ class bi_fm_index
  */
 //! \brief Deduces the dimensions of the text.
 template <std::ranges::Range text_t>
-bi_fm_index(text_t &&) -> bi_fm_index<text_layout{dimension_v<text_t> != 1}>;
+bi_fm_index(text_t &&) -> bi_fm_index<innermost_value_type_t<text_t>, text_layout{dimension_v<text_t> != 1}>;
 //!\}
 
 //!\}