[FEATURE] change cigar.assign_string parameter to string view

Author: eseiler

include/seqan3/alphabet/cigar/cigar.hpp

@@ -159,16 +159,26 @@ class cigar : public alphabet_tuple_base<cigar, uint32_t, exposition_only::cigar
     /*!\name Write functions
      * \{
      */
-    /*!\brief Assign from the string representation.
+    /*!\brief Assign from a contigous char array.
      * \details
-     * \experimentalapi{Experimental since version 3.1.}
+     *
+     * In order to avoid unnecessary copies, you can initialise a seqan3::cigar from two char pointers that point to a
+     * contigous char array that stores the cigar string.
+     *
+     * \include test/snippet/alphabet/cigar/cigar_assign_string.cpp
+     *
+     * \attention If the cigar count cannot be correctly read, `0P` is added instead to the cigar string. 
+     *            Adding 0 padding is not impacting the alignment that the cigar string represents but
+     *            keeps the number of cigar elements consistent with the input.  
+     *
+     * \experimentalapi{Experimental since version 3.2.}
      */
-    cigar & assign_string(small_string<11> const s) noexcept
+    cigar & assign_string(std::string_view input) noexcept
     {
         uint32_t num{};
-        auto [ptr, errc] = std::from_chars(s.data(), s.data() + 10, num);
+        auto [ptr, errc] = std::from_chars(input.data(), input.data() + input.size(), num);
 
-        if ((errc != std::errc{}) || (!char_is_valid_for<operation>(*ptr)) || (*(ptr + 1) != 0))
+        if ((errc != std::errc{}) || (!char_is_valid_for<operation>(*ptr)))
         {
             get<0>(*this) = 0;
             assign_char_to('P', get<1>(*this));

include/seqan3/io/sam_file/detail/cigar.hpp

@@ -279,7 +279,7 @@ template <seqan3::detail::pairwise_alignment alignment_type>
     std::ranges::for_each(cigar_vector,
                           [&result](auto & cig)
                           {
-                              result.append(cig.to_string());
+                              result.append(static_cast<std::string_view>(cig.to_string()));
                           });
     return result;
 }

include/seqan3/utility/container/small_string.hpp

@@ -362,6 +362,26 @@ class small_string : public small_vector<char, capacity_ + 1>
     {
         return str();
     }
+
+    /*!\brief Implicit conversion to std::string_view.
+     *
+     * It is the programmer's responsibility to ensure that the resulting string view does not outlive the string.
+     *
+     * ### Exceptions
+     *
+     * Strong exception guarantee. No data is modified.
+     *
+     * ### Complexity
+     *
+     * Constant.
+     *
+     * \experimentalapi{Experimental since version 3.1.}
+     * \sa https://en.cppreference.com/w/cpp/string/basic_string/operator_basic_string_view
+     */
+    constexpr operator std::string_view() const noexcept
+    {
+        return std::string_view{data_.data(), this->size()};
+    }
     //!\}
 
     /*!\name Input/output

test/snippet/alphabet/cigar/cigar_assign_string.cpp

@@ -0,0 +1,37 @@
+#include <seqan3/alphabet/cigar/cigar.hpp>
+#include <seqan3/core/debug_stream.hpp>
+
+int main()
+{
+    std::string cigar_str{"4S134M"}; // input
+
+    seqan3::cigar letter1{};
+    seqan3::cigar letter2{};
+
+    // Assign from string
+    // convenient but creates an unnecessary string copy "4S"
+    letter1.assign_string(cigar_str.substr(0, 2));
+    letter2.assign_string(cigar_str.substr(2, 4));
+    seqan3::debug_stream << letter1 << '\n'; // prints 4S
+    seqan3::debug_stream << letter2 << '\n'; // prints 134M
+
+    // Assign from std::string_view (No extra string copies)
+    // Version 1
+    letter1.assign_string(std::string_view{cigar_str}.substr(0, 2));
+    letter2.assign_string(std::string_view{cigar_str}.substr(2, 4));
+    seqan3::debug_stream << letter1 << '\n'; // prints 4S
+    seqan3::debug_stream << letter2 << '\n'; // prints 134M
+    // No extra string copiesersion 2
+    letter1.assign_string(/*std::string_view*/ {cigar_str.data(), 2});
+    letter2.assign_string(/*std::string_view*/ {cigar_str.data() + 2, 4});
+    seqan3::debug_stream << letter1 << '\n'; // prints 4S
+    seqan3::debug_stream << letter2 << '\n'; // prints 134M
+
+    // Assign from char array
+    letter2.assign_string("40S");
+    seqan3::debug_stream << letter2 << '\n'; // prints 40S
+
+    // Assign from seqan3::small_string
+    letter2.assign_string(letter1.to_string());
+    seqan3::debug_stream << letter2 << '\n'; // prints 4S
+}

test/snippet/alphabet/cigar/cigar_assign_string.err

@@ -0,0 +1,8 @@
+4S
+134M
+4S
+134M
+4S
+134M
+40S
+4S

test/unit/alphabet/cigar/cigar_test.cpp

@@ -51,10 +51,29 @@ TEST(cigar, to_string)
 
 TEST(cigar, assign_string)
 {
+    // assign from char array
     seqan3::cigar c1{};
     c1.assign_string("223M");
     EXPECT_EQ(uint32_t{223}, seqan3::to_rank(get<0>(c1)));
     EXPECT_EQ('M', get<1>(c1).to_char());
+
+    // assign from string
+    std::string s{"4S"};
+    c1.assign_string(s);
+    EXPECT_EQ(uint32_t{4}, seqan3::to_rank(get<0>(c1)));
+    EXPECT_EQ('S', get<1>(c1).to_char());
+
+    // assign from std::string_view
+    std::string v{s};
+    c1.assign_string(v);
+    EXPECT_EQ(uint32_t{4}, seqan3::to_rank(get<0>(c1)));
+    EXPECT_EQ('S', get<1>(c1).to_char());
+
+    // assign from small_string
+    seqan3::small_string<11> ss{"1234D"};
+    c1.assign_string(ss);
+    EXPECT_EQ(uint32_t{1234}, seqan3::to_rank(get<0>(c1)));
+    EXPECT_EQ('D', get<1>(c1).to_char());
 }
 
 TEST(cigar, constexpr_char_literal)

test/unit/utility/container/small_string_test.cpp

@@ -104,13 +104,20 @@ TEST(small_string, string)
     EXPECT_EQ(em.str(), "hello"s); // explicit
 }
 
-TEST(small_string, implicit_conversion)
+TEST(small_string, implicit_conversion_string)
 {
     seqan3::small_string em{"hello"};
     std::string str = em;
     EXPECT_EQ(str, "hello"s); // explicit
 }
 
+TEST(small_string, implicit_conversion_string_view)
+{
+    seqan3::small_string em{"hello"};
+    std::string_view str_view{em};
+    EXPECT_EQ(str_view, "hello"s); // explicit
+}
+
 constexpr bool erase_test()
 {
     seqan3::small_string em{"hello"};