[DOC] generalized extend-functions; expand the changelog; update incl…

…udes

Signed-off-by: Lydia Buntrock <lydia.buntrock@fu-berlin.de>

CHANGELOG.md

@@ -39,18 +39,21 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
 
 #### Search
 
-<<<<<<< HEAD
 * Added `seqan3::interleaved_bloom_filter`, a data structure that efficiently answers set-membership queries for
   multiple bins ([\#920](https://github.com/seqan/seqan3/pull/920)).
-=======
 *  The `extend_right()` function can now also handle `char const *`.
   ([\#1588](https://github.com/seqan/seqan3/pull/1588)).
->>>>>>> de9a3880... [FIX] shorten the function with a redirect; move log to the correct release
 
 ## API changes
 
 ## Notable Bug-fixes
 
+#### Search
+
+* The `seqan3::fm_index_cursor::extend_right()`, `seqan3::bi_fm_index_cursor::extend_right()` and
+  `seqan3::bi_fm_index_cursor::extend_left()` functions handle c-style strings without including the null character
+  ([\#1588](https://github.com/seqan/seqan3/pull/1588)).
+
 # 3.0.1
 
 Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.

include/seqan3/search/fm_index/bi_fm_index_cursor.hpp

@@ -16,7 +16,8 @@
 
 #include <sdsl/suffix_trees.hpp>
 
-#include <seqan3/alphabet/all.hpp>
+#include <seqan3/alphabet/adaptation/char.hpp>
+#include <seqan3/alphabet/concept.hpp>
 #include <seqan3/core/type_traits/range.hpp>
 #include <seqan3/range/views/join.hpp>
 #include <seqan3/range/views/slice.hpp>
@@ -438,9 +439,13 @@ class bi_fm_index_cursor
     }
 
     //!\overload
-    bool extend_right(char const * c) noexcept
+    template <typename char_type>
+    //!\cond
+        requires seqan3::detail::is_char_adaptation_v<char_type>
+    //!\endcond
+    bool extend_right(char_type const * cstring) noexcept
     {
-        return extend_right(std::string_view{c});
+        return extend_right(std::basic_string_view<char_type>{cstring});
     }
 
     /*!\brief Tries to extend the query by the character `c` to the left.
@@ -485,10 +490,15 @@ class bi_fm_index_cursor
     }
 
     //!\overload
-    bool extend_left(char const * c) noexcept
+    template <typename char_type>
+    //!\cond
+        requires seqan3::detail::is_char_adaptation_v<char_type>
+    //!\endcond
+    bool extend_left(char_type const * cstring) noexcept
     {
-        return extend_left(std::string_view{c});
+        return extend_left(std::basic_string_view<char_type>{cstring});
     }
+
     /*!\brief Tries to extend the query by `seq` to the right.
      * \tparam seq_t The type of range of the sequence to search; must model std::ranges::forward_range.
      * \param[in] seq Sequence to extend the query with to the right.

include/seqan3/search/fm_index/fm_index_cursor.hpp

@@ -19,6 +19,7 @@
 
 #include <range/v3/view/slice.hpp>
 
+#include <seqan3/alphabet/adaptation/char.hpp>
 #include <seqan3/alphabet/concept.hpp>
 #include <seqan3/core/type_traits/range.hpp>
 #include <seqan3/range/views/join.hpp>
@@ -282,9 +283,13 @@ class fm_index_cursor
     }
 
     //!\overload
-    bool extend_right(char const * c) noexcept
+    template <typename char_type>
+    //!\cond
+        requires detail::is_char_adaptation_v<char_type>
+    //!\endcond
+    bool extend_right(char_type const * cstring) noexcept
     {
-        return extend_right(std::string_view{c});
+        return extend_right(std::basic_string_view<char_type>{cstring});
     }
 
     /*!\brief Tries to extend the query by `seq` to the right.

test/unit/search/fm_index/bi_fm_index_aa27_test.cpp

@@ -8,6 +8,8 @@
 #include "fm_index_collection_test_template.hpp"
 #include "fm_index_test_template.hpp"
 
+#include <seqan3/alphabet/aminoacid/aa27.hpp>
+
 using t1 = std::pair<seqan3::bi_fm_index<seqan3::aa27, seqan3::text_layout::single>,
                      seqan3::aa27_vector>;
 INSTANTIATE_TYPED_TEST_SUITE_P(aa27, fm_index_test, t1, );

test/unit/search/fm_index/bi_fm_index_char_test.cpp

@@ -8,6 +8,8 @@
 #include "fm_index_collection_test_template.hpp"
 #include "fm_index_test_template.hpp"
 
+#include <seqan3/alphabet/adaptation/uint.hpp>
+
 using t1 = std::pair<seqan3::bi_fm_index<unsigned char, seqan3::text_layout::single>,
                      std::vector<unsigned char>>;
 INSTANTIATE_TYPED_TEST_SUITE_P(char, fm_index_test, t1, );

test/unit/search/fm_index/bi_fm_index_dna4_test.cpp

@@ -8,6 +8,8 @@
 #include "fm_index_collection_test_template.hpp"
 #include "fm_index_test_template.hpp"
 
+#include <seqan3/alphabet/nucleotide/dna4.hpp>
+
 using t1 = std::pair<seqan3::bi_fm_index<seqan3::dna4, seqan3::text_layout::single>,
                      seqan3::dna4_vector>;
 INSTANTIATE_TYPED_TEST_SUITE_P(dna4, fm_index_test, t1, );

test/unit/search/fm_index/fm_index_dna4_test.cpp

@@ -8,6 +8,9 @@
 #include "fm_index_collection_test_template.hpp"
 #include "fm_index_test_template.hpp"
 
+#include <seqan3/alphabet/nucleotide/dna4.hpp>
+#include <seqan3/alphabet/nucleotide/dna5.hpp>
+
 using t1 = std::pair<seqan3::fm_index<seqan3::dna4, seqan3::text_layout::single>, seqan3::dna4_vector>;
 INSTANTIATE_TYPED_TEST_SUITE_P(dna4, fm_index_test, t1, );
 using t2 = std::pair<seqan3::fm_index<seqan3::dna4, seqan3::text_layout::collection>, std::vector<seqan3::dna4_vector>>;

test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp

@@ -329,7 +329,7 @@ TYPED_TEST_P(fm_index_cursor_collection_test, locate_char_string)
 
     // extend_right()
     {
-        fm_index index{text};
+        seqan3::fm_index index{text};
         auto it1 = index.begin();
         auto it2 = index.begin();
 
@@ -338,7 +338,7 @@ TYPED_TEST_P(fm_index_cursor_collection_test, locate_char_string)
 
         EXPECT_TRUE(std::ranges::equal(it1.locate(), it2.locate())); // [22,9] == [22,9]
 
-        bi_fm_index b_index{text};
+        seqan3::bi_fm_index b_index{text};
         auto it3 = b_index.begin();
         auto it4 = b_index.begin();
 
@@ -349,7 +349,7 @@ TYPED_TEST_P(fm_index_cursor_collection_test, locate_char_string)
     }
     // extend_left()
     {
-        bi_fm_index b_index{text};
+        seqan3::bi_fm_index b_index{text};
         auto it3 = b_index.begin();
         auto it4 = b_index.begin();