[BUG] extend_right/left() needs char const * overload (#1588)

* [FIX] extend_right() needs `char const *` overload

* [TEST] add tests for issue #1473

* [FIX] missing initialisation added

CHANGELOG.md

@@ -71,6 +71,12 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
 
 ## 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

@@ -18,6 +18,7 @@
 
 #include <seqan3/alphabet/adaptation/char.hpp>
 #include <seqan3/alphabet/adaptation/uint.hpp>
+#include <seqan3/alphabet/concept.hpp>
 #include <seqan3/core/type_traits/range.hpp>
 #include <seqan3/range/views/slice.hpp>
 #include <seqan3/search/fm_index/bi_fm_index.hpp>
@@ -118,9 +119,9 @@ class bi_fm_index_cursor
     // need to store it twice. Once the cursor is switched, the information becomes invalid anyway.
 
     //!\brief Left suffix array interval of the parent node.
-    size_type parent_lb;
+    size_type parent_lb{};
     //!\brief Left suffix array interval of the parent node.
-    size_type parent_rb;
+    size_type parent_rb{};
     //!\brief Label of the last edge moved down. Needed for cycle_back() or cycle_front().
     sdsl_char_type _last_char;
     //\}
@@ -441,6 +442,16 @@ class bi_fm_index_cursor
         return false;
     }
 
+    //!\overload
+    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::basic_string_view<char_type>{cstring});
+    }
+
     /*!\brief Tries to extend the query by the character `c` to the left.
      * \tparam char_t Type of the character needs to be convertible to the character type `char_type` of the index.
      * \param[in] c Character to extend the query with to the left.
@@ -486,6 +497,16 @@ class bi_fm_index_cursor
         return false;
     }
 
+    //!\overload
+    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::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/slice.hpp>
@@ -86,15 +87,15 @@ class fm_index_cursor
     //!\}
 
     //!\brief Underlying FM index.
-    index_type const * index;
+    index_type const * index{nullptr};
     //!\brief Left suffix array interval of the parent node. Needed for cycle_back().
-    size_type parent_lb;
+    size_type parent_lb{};
     //!\brief Right suffix array interval of the parent node. Needed for cycle_back().
-    size_type parent_rb;
+    size_type parent_rb{};
     //!\brief Underlying index from the SDSL.
-    node_type node;
+    node_type node{};
     //!\brief Alphabet size of the index without delimiters
-    sdsl_sigma_type sigma;
+    sdsl_sigma_type sigma{};
 
     template <typename _index_t>
     friend class bi_fm_index_cursor;
@@ -290,6 +291,16 @@ class fm_index_cursor
         return false;
     }
 
+    //!\overload
+    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::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.

test/unit/search/fm_index_cursor/bi_fm_index_cursor_collection_test_template.hpp

@@ -222,5 +222,38 @@ TYPED_TEST_P(bi_fm_index_cursor_collection_test, to_rev_cursor)
     }
 }
 
+TYPED_TEST_P(bi_fm_index_cursor_collection_test, extend_const_char_pointer)
+{
+    using alphabet_type = typename TestFixture::alphabet_type;
+
+    // test case for https://github.com/seqan/seqan3/issues/1473
+    if constexpr (std::is_same<alphabet_type, char>::value)
+    {
+        typename TypeParam::index_type fm{this->text_col1}; // {"AACGATCGGA", "AACGATCGGA"}
+        char const * cg = "CG";
+
+        // extend_right()
+        {
+            TypeParam it1 = TypeParam(fm);
+            TypeParam it2 = TypeParam(fm);
+
+            it1.extend_right(cg);
+            it2.extend_right(seqan3::views::slice(this->text1, 1, 3));      // "CG"
+
+            EXPECT_TRUE(std::ranges::equal(it1.locate(), it2.locate()));
+        }
+        // extend_left()
+        {
+            auto it1 = TypeParam(fm);
+            auto it2 = TypeParam(fm);
+
+            it1.extend_left(cg);
+            it2.extend_right(seqan3::views::slice(this->text1, 1, 3));      // "CG"
+
+            EXPECT_TRUE(std::ranges::equal(it1.locate(), it2.locate()));
+        }
+    }
+}
+
 REGISTER_TYPED_TEST_SUITE_P(bi_fm_index_cursor_collection_test, cursor, extend, extend_char, extend_range,
-                            extend_and_cycle, extend_range_and_cycle, to_fwd_cursor, to_rev_cursor);
+                            extend_and_cycle, extend_range_and_cycle, to_fwd_cursor, to_rev_cursor, extend_const_char_pointer);

test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp

@@ -321,6 +321,27 @@ TYPED_TEST_P(fm_index_cursor_collection_test, lazy_locate)
     EXPECT_TRUE(std::ranges::equal(it.locate(), it.lazy_locate()));
 }
 
+TYPED_TEST_P(fm_index_cursor_collection_test, extend_const_char_pointer)
+{
+    using alphabet_type = typename TestFixture::alphabet_type;
+
+    // test case for https://github.com/seqan/seqan3/issues/1473
+    if constexpr (std::is_same<alphabet_type, char>::value)
+    {
+        typename TypeParam::index_type fm{this->text_col1}; // {"ACGACG", "ACGACG"}
+        char const * cg = "CG";
+
+        // extend_right()
+        TypeParam it1 = TypeParam(fm);
+        TypeParam it2 = TypeParam(fm);
+
+        it1.extend_right(cg);
+        it2.extend_right(seqan3::views::slice(this->text1, 1, 3));      // "CG"
+
+        EXPECT_TRUE(std::ranges::equal(it1.locate(), it2.locate()));    // [(0,1),(0,4),(1,4),(1,1)]
+    }
+}
+
 TYPED_TEST_P(fm_index_cursor_collection_test, concept_check)
 {
     EXPECT_TRUE(seqan3::fm_index_cursor_specialisation<TypeParam>);
@@ -329,4 +350,4 @@ TYPED_TEST_P(fm_index_cursor_collection_test, concept_check)
 REGISTER_TYPED_TEST_SUITE_P(fm_index_cursor_collection_test, ctr, begin, extend_right_range,
                             extend_right_range_empty_text, extend_right_char, extend_right_range_and_cycle,
                             extend_right_char_and_cycle, extend_right_and_cycle, query, last_rank, incomplete_alphabet,
-                            lazy_locate, concept_check);
+                            lazy_locate, extend_const_char_pointer, concept_check);