[MISC] Review 1

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<dna5, text_layout::collection> index; // we need to the alphabet and text layout before loading
+    bi_fm_index<dna5, text_layout::collection> index; // we need 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<dna5, text_layout::collection> index; // we need to the alphabet and text layout before loading
+    bi_fm_index<dna5, text_layout::collection> index; // we need 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<dna5, text_layout::collection> index; // we need to the alphabet and text layout before loading
+    bi_fm_index<dna5, text_layout::collection> index; // we need the alphabet and text layout before loading
     {
         std::ifstream is{index_path, 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::text_layout_mode,
                                          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::text_layout_mode,
                                           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/fm_index/bi_fm_index.hpp

@@ -57,7 +57,7 @@ namespace seqan3
  *            are reserved and may not be used in the text.
  */
 template <Semialphabet alphabet_t,
-          text_layout text_layout_mode,
+          text_layout text_layout_mode_,
           detail::SdslIndex sdsl_index_type_ = default_sdsl_index_type>
 class bi_fm_index
 {
@@ -79,17 +79,23 @@ 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.
-    using fm_index_type = fm_index<alphabet_t, text_layout_mode, sdsl_index_type>;
+    //!\brief The type of the underlying FM index for the original text.
+    using fm_index_type = fm_index<alphabet_t, text_layout_mode_, 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<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.
-    fm_index_type rev_fm;
+    rev_fm_index_type rev_fm;
 
 public:
+    //!\brief Indicates whether index is built over a collection.
+    static constexpr text_layout text_layout_mode = text_layout_mode_;
+
     /*!\name Text types
      * \{
      */
@@ -104,12 +110,12 @@ class bi_fm_index
      */
     //!\brief The type of the bidirectional cursor.
     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 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>;
 
-    //!\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;
@@ -160,7 +166,7 @@ class bi_fm_index
      */
     template <std::ranges::Range text_t>
     //!\cond
-        requires !is_collection
+        requires !static_cast<bool>(text_layout_mode)
     //!\endcond
     void construct(text_t && text)
     {
@@ -180,7 +186,7 @@ class bi_fm_index
     //!\overload
     template <std::ranges::Range text_t>
     //!\cond
-        requires is_collection
+        requires static_cast<bool>(text_layout_mode)
     //!\endcond
     void construct(text_t && text)
     {
@@ -294,7 +300,7 @@ class bi_fm_index
      *
      * No-throw guarantee.
      */
-    uni_cursor_type fwd_begin() const noexcept
+    fwd_cursor_type fwd_begin() const noexcept
     {
        return {fwd_fm};
     }
@@ -313,7 +319,7 @@ class bi_fm_index
      *
      * No-throw guarantee.
      */
-    uni_cursor_type rev_begin() const noexcept
+    rev_cursor_type rev_begin() const noexcept
     {
        return {rev_fm};
     }

include/seqan3/search/fm_index/bi_fm_index_cursor.hpp

@@ -69,11 +69,11 @@ class bi_fm_index_cursor
      */
     //!\brief Type for the unidirectional cursor on the original text.
     using fwd_cursor = fm_index_cursor<fm_index<typename index_type::char_type,
-                                                text_layout{index_type::is_collection},
+                                                index_type::text_layout_mode,
                                                 typename index_type::sdsl_index_type>>;
     //!\brief Type for the unidirectional cursor on the reversed text.
     using rev_cursor = fm_index_cursor<fm_index<typename index_type::char_type,
-                                                text_layout{index_type::is_collection},
+                                                index_type::text_layout_mode,
                                                 typename index_type::sdsl_index_type>>;
     //!\}
 
@@ -250,7 +250,7 @@ class bi_fm_index_cursor
     bi_fm_index_cursor(index_t const & _index) noexcept : index(&_index),
                                                           fwd_lb(0), fwd_rb(_index.size() - 1),
                                                           rev_lb(0), rev_rb(_index.size() - 1),
-                                                          sigma(_index.fwd_fm.index.sigma - index_t::is_collection),
+                                                          sigma(_index.fwd_fm.index.sigma - index_t::text_layout_mode),
                                                           depth(0)
     {}
     //\}
@@ -863,7 +863,7 @@ class bi_fm_index_cursor
     template <std::ranges::Range text_t>
     auto path_label(text_t && text) const noexcept
     //!\cond
-        requires !index_t::is_collection
+        requires !static_cast<bool>(index_t::text_layout_mode)
     //!\endcond
     {
         static_assert(std::ranges::InputRange<text_t>, "The text must model InputRange.");
@@ -880,7 +880,7 @@ class bi_fm_index_cursor
     template <std::ranges::Range text_t>
     auto path_label(text_t && text) const noexcept
     //!\cond
-        requires index_t::is_collection
+        requires static_cast<bool>(index_t::text_layout_mode)
     //!\endcond
     {
         static_assert(std::ranges::InputRange<text_t>, "The text collection must model InputRange.");
@@ -925,7 +925,7 @@ class bi_fm_index_cursor
      */
     std::vector<size_type> locate() const
     //!\cond
-        requires !index_t::is_collection
+        requires !static_cast<bool>(index_t::text_layout_mode)
     //!\endcond
     {
         assert(index != nullptr);
@@ -941,7 +941,7 @@ class bi_fm_index_cursor
     //!\overload
     std::vector<std::pair<size_type, size_type>> locate() const
     //!\cond
-        requires index_t::is_collection
+        requires static_cast<bool>(index_t::text_layout_mode)
     //!\endcond
     {
         assert(index != nullptr);
@@ -972,7 +972,7 @@ class bi_fm_index_cursor
      */
     auto lazy_locate() const
     //!\cond
-        requires !index_t::is_collection
+        requires !static_cast<bool>(index_t::text_layout_mode)
     //!\endcond
     {
         assert(index != nullptr);
@@ -987,7 +987,7 @@ class bi_fm_index_cursor
     //!\overload
     auto lazy_locate() const
     //!\cond
-        requires index_t::is_collection
+        requires static_cast<bool>(index_t::text_layout_mode)
     //!\endcond
     {
         assert(index != nullptr);

include/seqan3/search/fm_index/concept.hpp

@@ -97,7 +97,7 @@ SEQAN3_CONCEPT FmIndex = std::Semiregular<t> && requires (t index)
 
     // NOTE: circular dependency
     // requires FmIndexCursor<typename t::cursor_type>;
-    requires requires (t index, std::conditional_t<t::is_collection,
+    requires requires (t index, std::conditional_t<t::text_layout_mode,
                                                    std::vector<std::vector<dna4>>,
                                                    std::vector<dna4>> const text)
     {
@@ -151,7 +151,7 @@ SEQAN3_CONCEPT FmIndexCursor = std::Semiregular<t> && requires (t cur)
     requires requires (typename t::index_type const index) { { t(index) } };
 
     requires requires (t cur, dna4 const c, std::vector<dna4> const seq,
-                       std::conditional_t<t::index_type::is_collection,
+                       std::conditional_t<t::index_type::text_layout_mode,
                                           std::vector<std::vector<dna4>>,
                                           std::vector<dna4>> const text)
     {
@@ -165,7 +165,7 @@ SEQAN3_CONCEPT FmIndexCursor = std::Semiregular<t> && requires (t cur)
     { cur.last_rank()    } -> typename t::size_type;
     { cur.query_length() } -> typename t::size_type;
     { cur.count()        } -> typename t::size_type;
-    { cur.locate()       } -> std::conditional_t<t::index_type::is_collection,
+    { cur.locate()       } -> std::conditional_t<t::index_type::text_layout_mode,
                                                 std::vector<std::pair<typename t::size_type, typename t::size_type>>,
                                                 std::vector<typename t::size_type>>;
     { cur.lazy_locate()  } -> auto;

include/seqan3/search/fm_index/fm_index.hpp

@@ -100,7 +100,7 @@ enum text_layout : bool
 
 /*!\brief The SeqAn FM Index.
  * \implements seqan3::FmIndex
- * \tparam is_collection    Indicates whether this index works on a text collection or a single text.
+ * \tparam text_layout_mode Indicates whether this index works on a text collection or a single text.
  *                          See seqan3::text_layout.
  * \tparam sdsl_index_type_ The type of the underlying SDSL index, must model seqan3::SdslIndex.
  * \details
@@ -135,7 +135,7 @@ enum text_layout : bool
  * \endif
  */
 template <Semialphabet alphabet_t,
-          text_layout text_layout_mode,
+          text_layout text_layout_mode_,
           detail::SdslIndex sdsl_index_type_ = default_sdsl_index_type>
 class fm_index
 {
@@ -164,6 +164,9 @@ class fm_index
     sdsl::rank_support_sd<1> text_begin_rs;
 
 public:
+    //!\brief Indicates whether index is built over a collection.
+    static constexpr text_layout text_layout_mode = text_layout_mode_;
+
     /*!\name Member types
      * \{
      */
@@ -175,8 +178,6 @@ class fm_index
     using cursor_type = fm_index_cursor<fm_index<alphabet_t, text_layout_mode, sdsl_index_type>>;
     //!\}
 
-    //!\brief Indicates whether index is built over a collection.
-    static constexpr bool is_collection = text_layout_mode;
 
     template <typename bi_fm_index_t>
     friend class bi_fm_index_cursor;
@@ -258,7 +259,7 @@ class fm_index
      */
     template <std::ranges::Range text_t>
     //!\cond
-        requires !is_collection
+        requires !static_cast<bool>(text_layout_mode)
     //!\endcond
     void construct(text_t && text)
     {
@@ -306,7 +307,7 @@ class fm_index
     //!\overload
     template <std::ranges::Range text_t>
     //!\cond
-        requires is_collection
+        requires static_cast<bool>(text_layout_mode)
     //!\endcond
     void construct(text_t && text)
     {
@@ -500,14 +501,14 @@ class fm_index
                                    std::to_string(alphabet_size<alphabet_t>) + "."};
         }
 
-        bool tmp = is_collection;
+        bool tmp = text_layout_mode;
         archive(tmp);
-        if (tmp != is_collection)
+        if (tmp != text_layout_mode)
         {
             throw std::logic_error{std::string{"The fm_index was built over a "} +
                                    (tmp ? "text collection" : "single text") +
                                    " but it is being read into a fm_index expecting a " +
-                                   (is_collection ? "text collection." : "single text.")};
+                                   (text_layout_mode ? "text collection." : "single text.")};
         }
     }
     //!\endcond

include/seqan3/search/fm_index/fm_index_cursor.hpp

@@ -162,7 +162,7 @@ class fm_index_cursor
 
     //! \brief Construct from given index.
     fm_index_cursor(index_t const & _index) noexcept : index(&_index), node({0, _index.index.size() - 1, 0, 0}),
-                                                       sigma(_index.index.sigma - index_t::is_collection)
+                                                       sigma(_index.index.sigma - index_t::text_layout_mode)
     {}
     //\}
 
@@ -443,7 +443,7 @@ class fm_index_cursor
     template <std::ranges::Range text_t>
     auto path_label(text_t && text) const noexcept
     //!\cond
-        requires !index_t::is_collection
+        requires !static_cast<bool>(index_t::text_layout_mode)
     //!\endcond
     {
         static_assert(std::ranges::InputRange<text_t>, "The text must model InputRange.");
@@ -460,7 +460,7 @@ class fm_index_cursor
     template <std::ranges::Range text_t>
     auto path_label(text_t && text) const noexcept
     //!\cond
-        requires index_t::is_collection
+        requires static_cast<bool>(index_t::text_layout_mode)
     //!\endcond
     {
         static_assert(std::ranges::InputRange<text_t>, "The text collection must model InputRange.");
@@ -505,7 +505,7 @@ class fm_index_cursor
      */
     std::vector<size_type> locate() const
     //!\cond
-        requires !index_t::is_collection
+        requires !static_cast<bool>(index_t::text_layout_mode)
     //!\endcond
     {
         assert(index != nullptr);
@@ -521,7 +521,7 @@ class fm_index_cursor
     //!\overload
     std::vector<std::pair<size_type, size_type>> locate() const
     //!\cond
-        requires index_t::is_collection
+        requires static_cast<bool>(index_t::text_layout_mode)
     //!\endcond
     {
         assert(index != nullptr);
@@ -552,7 +552,7 @@ class fm_index_cursor
      */
     auto lazy_locate() const
     //!\cond
-        requires !index_t::is_collection
+        requires !static_cast<bool>(index_t::text_layout_mode)
     //!\endcond
     {
         assert(index != nullptr);
@@ -564,7 +564,7 @@ class fm_index_cursor
     //!\overload
     auto lazy_locate() const
     //!\cond
-        requires index_t::is_collection
+        requires static_cast<bool>(index_t::text_layout_mode)
     //!\endcond
     {
         assert(index != nullptr);