[WIP] Header only and attributes

seqan · Oct 23, 2024 · b80ff97 · b80ff97
1 parent 2ed20d8
commit b80ff97
Show file tree

Hide file tree

Showing 7 changed files with 45 additions and 93 deletions.
diff --git a/include/hibf/config.hpp b/include/hibf/config.hpp
@@ -12,7 +12,7 @@
 #include <cereal/access.hpp> // for access
 #include <cereal/cereal.hpp> // for make_nvp, CEREAL_NVP
 
-#include <hibf/misc/insert_iterator.hpp> // for insert_iterator
+#include <hibf/misc/insert_iterator.hpp>
 #include <hibf/platform.hpp>
 
 namespace seqan::hibf

diff --git a/include/hibf/interleaved_bloom_filter.hpp b/include/hibf/interleaved_bloom_filter.hpp
@@ -24,7 +24,6 @@
 #include <cereal/types/base_class.hpp> // for base_class
 
 #include <hibf/cereal/concepts.hpp>           // for cereal_archive
-#include <hibf/config.hpp>                    // for config
 #include <hibf/contrib/aligned_allocator.hpp> // for aligned_allocator
 #include <hibf/misc/bit_vector.hpp>           // for bit_vector
 #include <hibf/misc/counting_vector.hpp>      // for counting_vector
@@ -33,6 +32,10 @@
 
 namespace seqan::hibf
 {
+
+// config.hpp -> misc/insert_iterator.hpp (Needs interleaved_bloom_filter to be a complete class)
+struct config;
+
 /*!\brief A strong type that represents the number of bins for the seqan::hibf::interleaved_bloom_filter.
  * \ingroup ibf
  * \qualifier strong

diff --git a/include/hibf/misc/insert_iterator.hpp b/include/hibf/misc/insert_iterator.hpp
@@ -13,24 +13,15 @@
 #include <vector>     // for vector
 
 #include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set, hash
+#include <hibf/interleaved_bloom_filter.hpp>
 #include <hibf/platform.hpp>
+#include <hibf/sketch/hyperloglog.hpp>
 
 // IWYU pragma: private, include <hibf/config.hpp>
 
 namespace seqan::hibf
 {
 
-// hibf/interleaved_bloom_filter.hpp includes config.hpp, which includes insert_iterator.hpp
-// Hence, we need a forward declaration.
-class interleaved_bloom_filter;
-
-namespace sketch
-{
-
-class hyperloglog;
-
-}
-
 class insert_iterator
 {
 public:
@@ -64,10 +55,30 @@ class insert_iterator
         type{data_type::ibf}
     {}
 
-    constexpr insert_iterator(function_t & fun) : ptr{std::addressof(fun)}, type{data_type::function}
+    explicit constexpr insert_iterator(function_t & fun) : ptr{std::addressof(fun)}, type{data_type::function}
     {}
 
-    insert_iterator & operator=(uint64_t const value) noexcept;
+    [[gnu::always_inline, gnu::flatten]] constexpr insert_iterator & operator=(uint64_t const value) noexcept
+    {
+        assert(ptr != nullptr);
+
+        switch (type)
+        {
+        case data_type::unordered_set:
+            static_cast<set_t *>(ptr)->emplace(value);
+            break;
+        case data_type::sketch:
+            static_cast<sketch_t *>(ptr)->add(value);
+            break;
+        case data_type::ibf:
+            static_cast<ibf_t *>(ptr)->emplace(value, static_cast<bin_index>(ibf_bin_index));
+            break;
+        default:
+            assert(type == data_type::function);
+            static_cast<function_t *>(ptr)->operator()(value);
+        }
+        return *this;
+    }
 
     [[nodiscard]] constexpr insert_iterator & operator*() noexcept
     {

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -15,7 +15,6 @@ set (HIBF_SOURCE_FILES
      sketch/compute_sketches.cpp
      layout/graph.cpp
      layout/hierarchical_binning.cpp
-     misc/insert_iterator.cpp
      misc/print.cpp
      sketch/toolbox.cpp
      sketch/hyperloglog.cpp

diff --git a/src/interleaved_bloom_filter.cpp b/src/interleaved_bloom_filter.cpp
@@ -16,13 +16,19 @@
 #include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter, bin_count, bin_index, bin_size, hash_...
 #include <hibf/misc/bit_vector.hpp>          // for bit_vector
 #include <hibf/misc/divide_and_ceil.hpp>     // for divide_and_ceil
-#include <hibf/platform.hpp>                 // for HIBF_COMPILER_IS_GCC
-#include <hibf/sketch/compute_sketches.hpp>  // for compute_sketches
-#include <hibf/sketch/hyperloglog.hpp>       // for hyperloglog
+#include <hibf/misc/insert_iterator.hpp>
+#include <hibf/platform.hpp>                // for HIBF_COMPILER_IS_GCC
+#include <hibf/sketch/compute_sketches.hpp> // for compute_sketches
+#include <hibf/sketch/hyperloglog.hpp>      // for hyperloglog
 
 namespace seqan::hibf
 {
 
+#if HIBF_COMPILER_IS_GCC
+#    pragma GCC diagnostic push
+#    pragma GCC diagnostic ignored "-Wattributes"
+#endif // HIBF_COMPILER_IS_GCC
+
 interleaved_bloom_filter::interleaved_bloom_filter(seqan::hibf::bin_count bins_,
                                                    seqan::hibf::bin_size size,
                                                    seqan::hibf::hash_function_count funs)
@@ -133,12 +139,12 @@ inline auto interleaved_bloom_filter::emplace_impl(size_t const value, bin_index
         return exists;
 };
 
-void interleaved_bloom_filter::emplace(size_t const value, bin_index const bin) noexcept
+[[gnu::always_inline]] void interleaved_bloom_filter::emplace(size_t const value, bin_index const bin) noexcept
 {
     return emplace_impl<false>(value, bin);
 }
 
-bool interleaved_bloom_filter::emplace_exists(size_t const value, bin_index const bin) noexcept
+[[gnu::always_inline]] bool interleaved_bloom_filter::emplace_exists(size_t const value, bin_index const bin) noexcept
 {
     return emplace_impl<true>(value, bin);
 }
@@ -193,16 +199,9 @@ void interleaved_bloom_filter::increase_bin_number_to(seqan::hibf::bin_count con
     technical_bins = new_technical_bins;
 }
 
-#if HIBF_COMPILER_IS_GCC
-#    pragma GCC diagnostic push
-#    pragma GCC diagnostic ignored "-Wattributes"
-#endif // HIBF_COMPILER_IS_GCC
 [[gnu::always_inline]] bit_vector const &
 interleaved_bloom_filter::membership_agent_type::bulk_contains(size_t const value) & noexcept
 {
-#if HIBF_COMPILER_IS_GCC
-#    pragma GCC diagnostic pop
-#endif // HIBF_COMPILER_IS_GCC
     assert(ibf_ptr != nullptr);
     assert(result_buffer.size() == ibf_ptr->bin_count());
 
@@ -291,4 +290,8 @@ interleaved_bloom_filter::membership_agent_type::bulk_contains(size_t const valu
     return result_buffer;
 }
 
+#if HIBF_COMPILER_IS_GCC
+#    pragma GCC diagnostic pop
+#endif // HIBF_COMPILER_IS_GCC
+
 } // namespace seqan::hibf
diff --git a/src/misc/insert_iterator.cpp b/src/misc/insert_iterator.cpp
diff --git a/test/performance/ibf/interleaved_bloom_filter_construction_benchmark.cpp b/test/performance/ibf/interleaved_bloom_filter_construction_benchmark.cpp
@@ -15,6 +15,7 @@
 #include <utility>    // for move, pair
 #include <vector>     // for vector
 
+#include <hibf/config.hpp>                          // for config
 #include <hibf/contrib/robin_hood.hpp>              // for hash, unordered_map
 #include <hibf/contrib/std/chunk_view.hpp>          // for chunk, chunk_fn, chunk_view
 #include <hibf/contrib/std/detail/adaptor_base.hpp> // for operator|