Merge pull request #2048 from eseiler/feature/serialise_cursor

[FEATURE] Serialise index cursor
seqan · Aug 31, 2020 · 9babc11 · 9babc11
2 parents f6a3cc3 + 7f46653
commit 9babc11
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Showing 8 changed files with 111 additions and 5 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -73,6 +73,8 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
   ([\#1853](https://github.com/seqan/seqan3/pull/1853)).
 * Added `seqan3::search_cfg::on_result`, which allows providing a custom callback for the search algorithm
   ([\#2019](https://github.com/seqan/seqan3/pull/2019)).
+* The `seqan3::fm_index_cursor` and `seqan3::bi_fm_index_cursor` can be serialised
+  ([\#2048](https://github.com/seqan/seqan3/pull/2019)).
 
 ## API changes
 

diff --git a/include/seqan3/search/fm_index/bi_fm_index_cursor.hpp b/include/seqan3/search/fm_index/bi_fm_index_cursor.hpp
@@ -34,6 +34,7 @@ namespace seqan3
 /*!\brief The SeqAn Bidirectional FM Index Cursor.
  * \implements seqan3::bi_fm_index_cursor_specialisation
  * \tparam index_t The type of the underlying index; must model seqan3::bi_fm_index_specialisation.
+ * \implements seqan3::cerealisable
  * \details
  *
  * The cursor's interface provides searching a string both from left to right as well as from right to left in the
@@ -1022,6 +1023,28 @@ class bi_fm_index_cursor
                    return locate_result_value_type{sequence_rank-1, sequence_position};
                });
     }
+
+    /*!\cond DEV
+     * \brief Serialisation support function.
+     * \tparam archive_t Type of `archive`; must satisfy seqan3::cereal_archive.
+     * \param archive The archive being serialised from/to.
+     *
+     * \attention These functions are never called directly, see \ref serialisation for more details.
+     */
+    template <cereal_archive archive_t>
+    void CEREAL_SERIALIZE_FUNCTION_NAME(archive_t & archive)
+    {
+        archive(fwd_lb);
+        archive(fwd_rb);
+        archive(rev_lb);
+        archive(rev_rb);
+        archive(sigma);
+        archive(parent_lb);
+        archive(parent_rb);
+        archive(_last_char);
+        archive(depth);
+    }
+    //!\endcond
 };
 
 //!\}

diff --git a/include/seqan3/search/fm_index/detail/fm_index_cursor.hpp b/include/seqan3/search/fm_index/detail/fm_index_cursor.hpp
@@ -15,7 +15,7 @@
 #include <tuple>
 #include <type_traits>
 
-#include <seqan3/core/platform.hpp>
+#include <seqan3/core/concept/cereal.hpp>
 
 namespace seqan3::detail
 {
@@ -27,6 +27,7 @@ namespace seqan3::detail
 /*!\brief Internal representation of the node of an FM index cursor.
  * \ingroup fm_index
  * \tparam index_t The type of the underlying index; must satisfy seqan3::fm_index_specialisation.
+ * \implements seqan3::cerealisable
  */
 template <typename index_t>
 struct fm_index_cursor_node
@@ -61,6 +62,23 @@ struct fm_index_cursor_node
     {
         return !(*this == rhs);
     }
+
+    /*!\cond DEV
+     * \brief Serialisation support function.
+     * \tparam archive_t Type of `archive`; must satisfy seqan3::cereal_archive.
+     * \param archive The archive being serialised from/to.
+     *
+     * \attention These functions are never called directly, see \ref serialisation for more details.
+     */
+    template <cereal_archive archive_t>
+    void CEREAL_SERIALIZE_FUNCTION_NAME(archive_t & archive)
+    {
+        archive(lb);
+        archive(rb);
+        archive(depth);
+        archive(last_char);
+    }
+    //!\endcond
 };
 
 // std::tuple get_suffix_array_range(fm_index_cursor<index_t> const & it)

diff --git a/include/seqan3/search/fm_index/fm_index_cursor.hpp b/include/seqan3/search/fm_index/fm_index_cursor.hpp
@@ -35,6 +35,7 @@ namespace seqan3
 /*!\brief The SeqAn FM Index Cursor.
  * \implements seqan3::fm_index_cursor_specialisation
  * \tparam index_t The type of the underlying index; must model seqan3::fm_index_specialisation.
+ * \implements seqan3::cerealisable
  * \details
  *
  * The cursor's interface provides searching a string from left to right in the indexed text.
@@ -621,6 +622,23 @@ class fm_index_cursor
                    return locate_result_value_type{sequence_rank - 1, sequence_position};
                });
     }
+
+    /*!\cond DEV
+     * \brief Serialisation support function.
+     * \tparam archive_t Type of `archive`; must satisfy seqan3::cereal_archive.
+     * \param archive The archive being serialised from/to.
+     *
+     * \attention These functions are never called directly, see \ref serialisation for more details.
+     */
+    template <cereal_archive archive_t>
+    void CEREAL_SERIALIZE_FUNCTION_NAME(archive_t & archive)
+    {
+        archive(parent_lb);
+        archive(parent_rb);
+        archive(node);
+        archive(sigma);
+    }
+    //!\endcond
 };
 
 //!\}

diff --git a/test/unit/search/fm_index_cursor/bi_fm_index_cursor_collection_test_template.hpp b/test/unit/search/fm_index_cursor/bi_fm_index_cursor_collection_test_template.hpp
@@ -14,6 +14,7 @@
 #include <seqan3/core/detail/debug_stream_tuple.hpp>
 #include <seqan3/range/views/slice.hpp>
 #include <seqan3/search/fm_index/bi_fm_index_cursor.hpp>
+#include <seqan3/test/cereal.hpp>
 #include <seqan3/test/expect_range_eq.hpp>
 
 #include "../helper.hpp"
@@ -220,5 +221,16 @@ TYPED_TEST_P(bi_fm_index_cursor_collection_test, extend_const_char_pointer)
     }
 }
 
+TYPED_TEST_P(bi_fm_index_cursor_collection_test, serialisation)
+{
+    typename TypeParam::index_type bi_fm{this->text_col2};
+
+    TypeParam it = TypeParam(bi_fm);
+    it.extend_left(seqan3::views::slice(this->text, 1, 3));
+
+    seqan3::test::do_serialisation(it);
+}
+
 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, extend_const_char_pointer);
+                            extend_and_cycle, extend_range_and_cycle, to_fwd_cursor, extend_const_char_pointer,
+                            serialisation);
diff --git a/test/unit/search/fm_index_cursor/bi_fm_index_cursor_test_template.hpp b/test/unit/search/fm_index_cursor/bi_fm_index_cursor_test_template.hpp
@@ -14,6 +14,7 @@
 #include <seqan3/core/detail/debug_stream_tuple.hpp>
 #include <seqan3/range/views/slice.hpp>
 #include <seqan3/search/fm_index/bi_fm_index_cursor.hpp>
+#include <seqan3/test/cereal.hpp>
 #include <seqan3/test/expect_range_eq.hpp>
 
 #include "../helper.hpp"
@@ -184,5 +185,15 @@ TYPED_TEST_P(bi_fm_index_cursor_test, to_fwd_cursor)
     }
 }
 
+TYPED_TEST_P(bi_fm_index_cursor_test, serialisation)
+{
+    typename TypeParam::index_type bi_fm{this->text};
+
+    TypeParam it(bi_fm);
+    it.extend_left(seqan3::views::slice(this->text, 1, 3));
+
+    seqan3::test::do_serialisation(it);
+}
+
 REGISTER_TYPED_TEST_SUITE_P(bi_fm_index_cursor_test, cursor, extend, extend_char, extend_range, extend_and_cycle,
-                            extend_range_and_cycle, to_fwd_cursor);
+                            extend_range_and_cycle, to_fwd_cursor, serialisation);
diff --git a/test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp b/test/unit/search/fm_index_cursor/fm_index_cursor_collection_test_template.hpp
@@ -11,6 +11,7 @@
 #include <seqan3/range/views/slice.hpp>
 #include <seqan3/search/fm_index/concept.hpp>
 #include <seqan3/std/algorithm>
+#include <seqan3/test/cereal.hpp>
 #include <seqan3/test/expect_range_eq.hpp>
 
 #include <sdsl/csa_wt.hpp>
@@ -348,7 +349,17 @@ TYPED_TEST_P(fm_index_cursor_collection_test, concept_check)
     EXPECT_TRUE(seqan3::fm_index_cursor_specialisation<TypeParam>);
 }
 
+TYPED_TEST_P(fm_index_cursor_collection_test, serialisation)
+{
+    typename TypeParam::index_type fm{this->text_col4};
+
+    TypeParam it(fm);
+    it.extend_right(seqan3::views::slice(this->text1, 0, 3));
+
+    seqan3::test::do_serialisation(it);
+}
+
 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, extend_const_char_pointer, concept_check);
+                            lazy_locate, extend_const_char_pointer, concept_check, serialisation);
diff --git a/test/unit/search/fm_index_cursor/fm_index_cursor_test_template.hpp b/test/unit/search/fm_index_cursor/fm_index_cursor_test_template.hpp
@@ -11,6 +11,7 @@
 #include <seqan3/range/views/slice.hpp>
 #include <seqan3/search/fm_index/concept.hpp>
 #include <seqan3/std/algorithm>
+#include <seqan3/test/cereal.hpp>
 #include <seqan3/test/expect_range_eq.hpp>
 
 #include <sdsl/csa_wt.hpp>
@@ -300,6 +301,16 @@ TYPED_TEST_P(fm_index_cursor_test, concept_check)
     EXPECT_TRUE(seqan3::fm_index_cursor_specialisation<TypeParam>);
 }
 
+TYPED_TEST_P(fm_index_cursor_test, serialisation)
+{
+    typename TypeParam::index_type fm{this->text1};
+
+    TypeParam it = TypeParam(fm);
+    it.extend_right(seqan3::views::slice(this->text1, 0, 3));
+
+    seqan3::test::do_serialisation(it);
+}
+
 REGISTER_TYPED_TEST_SUITE_P(fm_index_cursor_test, ctr, begin, extend_right_range, 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);
+                            last_rank, incomplete_alphabet, lazy_locate, concept_check, serialisation);