[FIX] Add data access for containers

seqan · Aug 14, 2019 · 25d06a0 · 25d06a0
1 parent 22539ca
commit 25d06a0
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Showing 4 changed files with 52 additions and 21 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,6 +29,10 @@ If possible, provide tooling that performs the changes, e.g. a shell-script.
 
 If you included `<seqan3/core/type_list.hpp>` you need to change the path to `<seqan3/core/type_list/type_list.hpp>`.
 
+### The `data()` function of `seqan3::concatenated_sequences` has been deprecated
+
+Use `raw_data()` instead.
+
 ## Notable Bug-fixes
 
 # 3.0.0 ("Escala")

diff --git a/include/seqan3/range/container/bitcompressed_vector.hpp b/include/seqan3/range/container/bitcompressed_vector.hpp
@@ -518,6 +518,19 @@ class bitcompressed_vector
         return (*this)[size()-1];
     }
 
+    //!\brief Direct access to the underlying SDSL vector.
+    constexpr data_type & raw_data() noexcept
+    {
+        return data;
+    }
+
+    //!\copydoc raw_data()
+    constexpr data_type const & raw_data() const noexcept
+    {
+        return data;
+    }
+    //!\}
+
     /*!\name Capacity
      * \{
      */
@@ -964,37 +977,37 @@ class bitcompressed_vector
     //!\brief Checks whether `*this` is equal to `rhs`.
     constexpr bool operator==(bitcompressed_vector const & rhs) const noexcept
     {
-        return data == rhs.data;
+        return raw_data() == rhs.raw_data();
     }
 
     //!\brief Checks whether `*this` is not equal to `rhs`.
     constexpr bool operator!=(bitcompressed_vector const & rhs) const noexcept
     {
-        return data != rhs.data;
+        return raw_data() != rhs.raw_data();
     }
 
     //!\brief Checks whether `*this` is less than `rhs`.
     constexpr bool operator<(bitcompressed_vector const & rhs) const noexcept
     {
-        return data < rhs.data;
+        return raw_data() < rhs.raw_data();
     }
 
     //!\brief Checks whether `*this` is greater than `rhs`.
     constexpr bool operator>(bitcompressed_vector const & rhs) const noexcept
     {
-        return data > rhs.data;
+        return raw_data() > rhs.raw_data();
     }
 
     //!\brief Checks whether `*this` is less than or equal to `rhs`.
     constexpr bool operator<=(bitcompressed_vector const & rhs) const noexcept
     {
-        return data <= rhs.data;
+        return raw_data() <= rhs.raw_data();
     }
 
     //!\brief Checks whether `*this` is greater than or equal to `rhs`.
     constexpr bool operator>=(bitcompressed_vector const & rhs) const noexcept
     {
-        return data >= rhs.data;
+        return raw_data() >= rhs.raw_data();
     }
     //!\}
 
@@ -1008,7 +1021,7 @@ class bitcompressed_vector
     template <CerealArchive archive_t>
     void CEREAL_SERIALIZE_FUNCTION_NAME(archive_t & archive)
     {
-        archive(data); //TODO: data not yet serialisable
+        archive(data);
     }
     //!\endcond
 };

diff --git a/include/seqan3/range/container/concatenated_sequences.hpp b/include/seqan3/range/container/concatenated_sequences.hpp
@@ -53,7 +53,7 @@ namespace seqan3
  * * Better cache locality when parsing the sequences linearly (and often also on random access).
  * * Constant time access to the concatenation of the sequences via concat().
  * * This access is also writable so that certain transformations can be done globally, instead of element-wise.
- * * Also direct access to the delimiters via data() [this is used by some algorithms].
+ * * Also direct access to the delimiters via raw_data() [this is used by some algorithms].
  *
  * The disadvantages are:
  *
@@ -602,16 +602,30 @@ class concatenated_sequences
      *
      * This exact representation of the data is implementation defined. Do not rely on it for API stability.
      */
-    std::pair<decltype(data_values) &, decltype(data_delimiters) &> data()
+    std::pair<decltype(data_values) &, decltype(data_delimiters) &> raw_data()
     {
         return {data_values, data_delimiters};
     }
 
-    //!\copydoc data()
-    std::pair<decltype(data_values) const &, decltype(data_delimiters) const &> data() const
+    //!\copydoc raw_data()
+    std::pair<decltype(data_values) const &, decltype(data_delimiters) const &> raw_data() const
     {
         return {std::as_const(data_values), std::as_const(data_delimiters)};
     }
+
+    //!\copydoc raw_data()
+    //!\deprecated Use raw_data() instead.
+    SEQAN3_DEPRECATED_310 std::pair<decltype(data_values) &, decltype(data_delimiters) &> data()
+    {
+        return raw_data();
+    }
+
+    //!\copydoc raw_data()
+    //!\deprecated Use raw_data() instead.
+    SEQAN3_DEPRECATED_310 std::pair<decltype(data_values) const &, decltype(data_delimiters) const &> data() const
+    {
+        return raw_data();
+    }
     //!\}
 
     /*!\name Capacity
@@ -1243,37 +1257,37 @@ class concatenated_sequences
     //!\brief Checks whether `*this` is equal to `rhs`.
     constexpr bool operator==(concatenated_sequences const & rhs) const noexcept
     {
-        return data() == rhs.data();
+        return raw_data() == rhs.raw_data();
     }
 
     //!\brief Checks whether `*this` is not equal to `rhs`.
     constexpr bool operator!=(concatenated_sequences const & rhs) const noexcept
     {
-        return data() != rhs.data();
+        return raw_data() != rhs.raw_data();
     }
 
     //!\brief Checks whether `*this` is less than `rhs`.
     constexpr bool operator<(concatenated_sequences const & rhs) const noexcept
     {
-        return data() < rhs.data();
+        return raw_data() < rhs.raw_data();
     }
 
     //!\brief Checks whether `*this` is greater than `rhs`.
     constexpr bool operator>(concatenated_sequences const & rhs) const noexcept
     {
-        return data() > rhs.data();
+        return raw_data() > rhs.raw_data();
     }
 
     //!\brief Checks whether `*this` is less than or equal to `rhs`.
     constexpr bool operator<=(concatenated_sequences const & rhs) const noexcept
     {
-        return data() <= rhs.data();
+        return raw_data() <= rhs.data();
     }
 
     //!\brief Checks whether `*this` is greater than or equal to `rhs`.
     constexpr bool operator>=(concatenated_sequences const & rhs) const noexcept
     {
-        return data() >= rhs.data();
+        return raw_data() >= rhs.raw_data();
     }
     //!\}
 

diff --git a/test/unit/range/container/container_of_container_test.cpp b/test/unit/range/container/container_of_container_test.cpp
@@ -152,10 +152,10 @@ TYPED_TEST(container_of_container, element_access)
         EXPECT_EQ(dna4_vector(t2.concat()), "ACGTACGTGAGGA"_dna4);
 
         // data
-        EXPECT_EQ(std::get<0>(t1.data()), "ACGTACGTGAGGA"_dna4);
-        EXPECT_EQ(std::get<0>(t2.data()), "ACGTACGTGAGGA"_dna4);
-        EXPECT_EQ(std::get<1>(t1.data()), (std::vector<size_type>{0, 4, 8, 13}));
-        EXPECT_EQ(std::get<1>(t2.data()), (std::vector<size_type>{0, 4, 8, 13}));
+        EXPECT_EQ(std::get<0>(t1.raw_data()), "ACGTACGTGAGGA"_dna4);
+        EXPECT_EQ(std::get<0>(t2.raw_data()), "ACGTACGTGAGGA"_dna4);
+        EXPECT_EQ(std::get<1>(t1.raw_data()), (std::vector<size_type>{0, 4, 8, 13}));
+        EXPECT_EQ(std::get<1>(t2.raw_data()), (std::vector<size_type>{0, 4, 8, 13}));
     }
 
 }