[MISC] Rename hibf namespace to seqan::hibf

include/hibf/all.hpp

@@ -11,7 +11,7 @@
  */
 
 /*!\defgroup search_dream_index DREAM Index
- * \brief Provides hibf::interleaved_bloom_filter.
+ * \brief Provides seqan::hibf::interleaved_bloom_filter.
  * \ingroup search
  * \see search
  */

include/hibf/config.hpp

@@ -21,7 +21,7 @@
 #include <cereal/access.hpp> // for access
 #include <cereal/cereal.hpp> // for make_nvp, CEREAL_NVP
 
-namespace hibf
+namespace seqan::hibf
 {
 
 using insert_iterator = std::insert_iterator<robin_hood::unordered_flat_set<uint64_t>>;
@@ -111,4 +111,4 @@ struct config
     }
 };
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/contrib/aligned_allocator.hpp

@@ -22,7 +22,7 @@
 #    pragma GCC warning "Non-C++17 compliant compiler! Please open an issue with your compiler and platform!"
 #endif // __cpp_aligned_new < 201606
 
-namespace hibf::contrib
+namespace seqan::hibf::contrib
 {
 
 /*!\brief Allocates uninitialized storage whose memory-alignment is specified by *alignment*.
@@ -151,14 +151,14 @@ class aligned_allocator
     }
 
     /*!\brief Deallocates the storage referenced by the pointer p, which must be a pointer obtained by an earlier call
-     * to hibf::aligned_allocator::allocate.
+     * to seqan::hibf::aligned_allocator::allocate.
      *
      * \param[in] p The pointer to the memory to be deallocated.
      * \param[in] n The number of elements to be deallocated.
      *
      * \details
      *
-     * The argument `n` must be equal to the first argument of the call to hibf::aligned_allocator::allocate that
+     * The argument `n` must be equal to the first argument of the call to seqan::hibf::aligned_allocator::allocate that
      * originally produced `p`, otherwise the behavior is undefined. This function calls
      * [operator delete](https://en.cppreference.com/w/cpp/memory/new/operator_delete) to deallocate the memory of
      * specified size.
@@ -237,4 +237,4 @@ class aligned_allocator
     //!\}
 };
 
-} // namespace hibf::contrib
+} // namespace seqan::hibf::contrib

include/hibf/detail/build/bin_size_in_bits.hpp

@@ -6,7 +6,7 @@
 // --------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Implements hibf::bin_size_in_bits.
+ * \brief Implements seqan::hibf::bin_size_in_bits.
  * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
  */
 
@@ -17,7 +17,7 @@
 
 #include <hibf/platform.hpp>
 
-namespace hibf
+namespace seqan::hibf
 {
 
 struct bin_size_parameters
@@ -35,4 +35,4 @@ inline size_t bin_size_in_bits(bin_size_parameters const & params)
     return result;
 }
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/build/build_data.hpp

@@ -17,14 +17,14 @@
 #include <hibf/detail/build/node_data.hpp> // for node_data
 #include <hibf/detail/timer.hpp>           // for concurrent, timer
 
-namespace hibf
+namespace seqan::hibf
 {
 
 struct build_data
 {
     std::atomic<size_t> ibf_number{};
 
-    hibf::config const & config;
+    seqan::hibf::config const & config;
 
     lemon::ListDigraph ibf_graph{};
     lemon::ListDigraph::NodeMap<node_data> node_map{ibf_graph};
@@ -46,4 +46,4 @@ struct build_data
     }
 };
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/build/chopper_pack_record.hpp

@@ -13,7 +13,7 @@
 
 #include <hibf/platform.hpp>
 
-namespace hibf
+namespace seqan::hibf
 {
 
 struct chopper_pack_record
@@ -45,4 +45,4 @@ struct chopper_pack_record
     }
 };
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/build/compute_kmers.hpp

@@ -6,7 +6,7 @@
 // --------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Implements hibf::compute_kmers.
+ * \brief Implements seqan::hibf::compute_kmers.
  * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
  */
 
@@ -18,11 +18,11 @@
 #include <hibf/detail/build/build_data.hpp> // for build_data
 #include <hibf/detail/layout/layout.hpp>    // for layout
 
-namespace hibf
+namespace seqan::hibf
 {
 
 void compute_kmers(robin_hood::unordered_flat_set<uint64_t> & kmers,
                    build_data const & data,
                    layout::layout::user_bin const & record);
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/build/construct_ibf.hpp

@@ -16,14 +16,14 @@
 #include <hibf/detail/build/build_data.hpp>  // for build_data
 #include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter
 
-namespace hibf
+namespace seqan::hibf
 {
 
-hibf::interleaved_bloom_filter construct_ibf(robin_hood::unordered_flat_set<uint64_t> & parent_kmers,
-                                             robin_hood::unordered_flat_set<uint64_t> & kmers,
-                                             size_t const number_of_bins,
-                                             lemon::ListDigraph::Node const & node,
-                                             build_data & data,
-                                             bool is_root);
+seqan::hibf::interleaved_bloom_filter construct_ibf(robin_hood::unordered_flat_set<uint64_t> & parent_kmers,
+                                                    robin_hood::unordered_flat_set<uint64_t> & kmers,
+                                                    size_t const number_of_bins,
+                                                    lemon::ListDigraph::Node const & node,
+                                                    build_data & data,
+                                                    bool is_root);
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/build/initialise_build_tree.hpp

@@ -6,7 +6,7 @@
 // --------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Implements hibf::initialise_build_tree.
+ * \brief Implements seqan::hibf::initialise_build_tree.
  * \author Svenja Mehringer <svenja.mehringer AT fu-berlin.de>
  */
 
@@ -17,11 +17,11 @@
 #include <hibf/detail/build/node_data.hpp> // for node_data
 #include <hibf/detail/layout/layout.hpp>   // for layout
 
-namespace hibf
+namespace seqan::hibf
 {
 
 void initialise_build_tree(layout::layout & hibf_layout,
                            lemon::ListDigraph & ibf_graph,
                            lemon::ListDigraph::NodeMap<node_data> & node_map);
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/build/insert_into_ibf.hpp

@@ -16,18 +16,18 @@
 #include <hibf/detail/timer.hpp>             // for concurrent, timer
 #include <hibf/interleaved_bloom_filter.hpp> // for interleaved_bloom_filter
 
-namespace hibf
+namespace seqan::hibf
 {
 
 // automatically does naive splitting if number_of_bins > 1
 void insert_into_ibf(robin_hood::unordered_flat_set<uint64_t> const & kmers,
                      size_t const number_of_bins,
                      size_t const bin_index,
-                     hibf::interleaved_bloom_filter & ibf,
+                     seqan::hibf::interleaved_bloom_filter & ibf,
                      timer<concurrent::yes> & fill_ibf_timer);
 
 void insert_into_ibf(build_data const & data,
                      layout::layout::user_bin const & record,
-                     hibf::interleaved_bloom_filter & ibf);
+                     seqan::hibf::interleaved_bloom_filter & ibf);
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/build/node_data.hpp

@@ -16,7 +16,7 @@
 
 #include <hibf/detail/layout/layout.hpp> // for operator==, layout
 
-namespace hibf
+namespace seqan::hibf
 {
 
 struct node_data // rename:ibf_data? or ibf_node_data
@@ -47,4 +47,4 @@ struct node_data // rename:ibf_data? or ibf_node_data
     }
 };
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/build/update_content_node_data.hpp

@@ -6,7 +6,7 @@
 // --------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Implements hibf::update_content_node_data.
+ * \brief Implements seqan::hibf::update_content_node_data.
  * \author Svenja Mehringer <svenja.mehringer AT fu-berlin.de>
  */
 
@@ -19,11 +19,11 @@
 #include <hibf/detail/build/node_data.hpp> // for node_data
 #include <hibf/detail/layout/layout.hpp>   // for layout
 
-namespace hibf
+namespace seqan::hibf
 {
 
 void update_content_node_data(std::vector<layout::layout::user_bin> && layout_user_bins,
                               lemon::ListDigraph & ibf_graph,
                               lemon::ListDigraph::NodeMap<node_data> & node_map);
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/build/update_header_node_data.hpp

@@ -6,7 +6,7 @@
 // --------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Implements hibf::update_header_node_data.
+ * \brief Implements seqan::hibf::update_header_node_data.
  * \author Svenja Mehringer <svenja.mehringer AT fu-berlin.de>
  */
 
@@ -19,11 +19,11 @@
 #include <hibf/detail/build/node_data.hpp> // for node_data
 #include <hibf/detail/layout/layout.hpp>   // for layout
 
-namespace hibf
+namespace seqan::hibf
 {
 
 void update_header_node_data(std::vector<layout::layout::max_bin> && header_max_bins,
                              lemon::ListDigraph & ibf_graph,
                              lemon::ListDigraph::NodeMap<node_data> & node_map);
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/build/update_parent_kmers.hpp

@@ -6,7 +6,7 @@
 // --------------------------------------------------------------------------------------------------
 
 /*!\file
- * \brief Implements hibf::update_parent_kmers.
+ * \brief Implements seqan::hibf::update_parent_kmers.
  * \author Svenja Mehringer <svenja.mehringer AT fu-berlin.de>
  */
 #pragma once
@@ -17,7 +17,7 @@
 #include <hibf/detail/timer.hpp>       // for concurrent, timer
 #include <hibf/platform.hpp>
 
-namespace hibf
+namespace seqan::hibf
 {
 
 inline void update_parent_kmers(robin_hood::unordered_flat_set<uint64_t> & parent_kmers,
@@ -31,4 +31,4 @@ inline void update_parent_kmers(robin_hood::unordered_flat_set<uint64_t> & paren
     merge_kmers_timer += local_merge_kmers_timer;
 }
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/build/update_user_bins.hpp

@@ -13,12 +13,12 @@
 
 #include <hibf/detail/layout/layout.hpp> // for layout
 
-namespace hibf
+namespace seqan::hibf
 {
 
 inline void update_user_bins(std::vector<int64_t> & filename_indices, layout::layout::user_bin const & record)
 {
     std::fill_n(filename_indices.begin() + record.storage_TB_id, record.number_of_technical_bins, record.idx);
 }
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/cereal/concepts.hpp

@@ -11,7 +11,7 @@
 
 #include <cereal/details/helpers.hpp> // for InputArchiveBase, OutputArchiveBase
 
-namespace hibf
+namespace seqan::hibf
 {
 
 template <typename t>
@@ -23,4 +23,4 @@ concept cereal_input_archive = std::is_base_of_v<cereal::detail::InputArchiveBas
 template <typename t>
 concept cereal_archive = cereal_output_archive<t> || cereal_input_archive<t>;
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/data_store.hpp

@@ -11,7 +11,7 @@
 #include <hibf/detail/layout/layout.hpp>      // for layout
 #include <hibf/detail/sketch/hyperloglog.hpp> // for hyperloglog
 
-namespace hibf
+namespace seqan::hibf
 {
 
 struct data_store
@@ -79,4 +79,4 @@ struct data_store
     //!\}
 };
 
-} // namespace hibf
+} // namespace seqan::hibf

include/hibf/detail/layout/compute_fpr_correction.hpp

@@ -5,7 +5,7 @@
 
 #include <hibf/platform.hpp>
 
-namespace hibf::layout
+namespace seqan::hibf::layout
 {
 
 struct fpr_correction_parameters
@@ -20,4 +20,4 @@ struct fpr_correction_parameters
  */
 std::vector<double> compute_fpr_correction(fpr_correction_parameters const & params);
 
-} // namespace hibf::layout
+} // namespace seqan::hibf::layout

include/hibf/detail/layout/compute_layout.hpp

@@ -7,7 +7,7 @@
 #include <hibf/detail/layout/layout.hpp>      // for layout
 #include <hibf/detail/sketch/hyperloglog.hpp> // for hyperloglog
 
-namespace hibf::layout
+namespace seqan::hibf::layout
 {
 
 /*!\brief Computes the layout and stores the kmer_counts and sketches in the respective vectors for further use.
@@ -21,4 +21,4 @@ compute_layout(config const & config, std::vector<size_t> & kmer_counts, std::ve
 
 layout compute_layout(config const & config);
 
-} // namespace hibf::layout
+} // namespace seqan::hibf::layout

include/hibf/detail/layout/execute.hpp

@@ -5,9 +5,9 @@
 #include <hibf/config.hpp>            // for config
 #include <hibf/detail/data_store.hpp> // for data_store
 
-namespace hibf
+namespace seqan::hibf
 {
 
 size_t execute(config const &, data_store &);
 
-} // namespace hibf
+} // namespace seqan::hibf