Merge pull request #69 from eseiler/misc/layout_execute

[MISC] Remove layout::execute
seqan · Sep 4, 2023 · 3188cec · 3188cec · vercel · Sep 4, 2023
2 parents a8966ca + 192670b
commit 3188cec
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Showing 4 changed files with 13 additions and 45 deletions.
diff --git a/include/hibf/layout/execute.hpp b/include/hibf/layout/execute.hpp
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -3,7 +3,6 @@ set (HIBF_SOURCE_FILES
      config.cpp
      layout/simple_binning.cpp
      layout/layout.cpp
-     layout/execute.cpp
      layout/compute_fpr_correction.cpp
      layout/compute_layout.cpp
      layout/graph.cpp

diff --git a/src/layout/compute_layout.cpp b/src/layout/compute_layout.cpp
@@ -7,14 +7,15 @@
 #include <utility>    // for addressof
 #include <vector>     // for vector
 
-#include <hibf/config.hpp>                      // for config
-#include <hibf/contrib/robin_hood.hpp>          // for unordered_flat_set
-#include <hibf/layout/compute_layout.hpp>       // for compute_layout
-#include <hibf/layout/data_store.hpp>           // for data_store
-#include <hibf/layout/execute.hpp>              // for execute
-#include <hibf/layout/layout.hpp>               // for layout
-#include <hibf/sketch/estimate_kmer_counts.hpp> // for estimate_kmer_counts
-#include <hibf/sketch/hyperloglog.hpp>          // for hyperloglog
+#include <hibf/config.hpp>                        // for config
+#include <hibf/contrib/robin_hood.hpp>            // for unordered_flat_set
+#include <hibf/layout/compute_fpr_correction.hpp> // for compute_fpr_correction
+#include <hibf/layout/compute_layout.hpp>         // for compute_layout
+#include <hibf/layout/data_store.hpp>             // for data_store
+#include <hibf/layout/hierarchical_binning.hpp>   // for hierarchical_binning
+#include <hibf/layout/layout.hpp>                 // for layout
+#include <hibf/sketch/estimate_kmer_counts.hpp>   // for estimate_kmer_counts
+#include <hibf/sketch/hyperloglog.hpp>            // for hyperloglog
 
 namespace seqan::hibf::layout
 {
@@ -55,9 +56,11 @@ compute_layout(config const & config, std::vector<size_t> & kmer_counts, std::ve
                      .hibf_layout = &resulting_layout,
                      .kmer_counts = std::addressof(kmer_counts),
                      .sketches = std::addressof(sketches)};
+    store.fpr_correction = compute_fpr_correction({.fpr = config.maximum_false_positive_rate,
+                                                   .hash_count = config.number_of_hash_functions,
+                                                   .t_max = config.tmax});
 
-    size_t const max_hibf_id = seqan::hibf::layout::execute(config, store);
-    store.hibf_layout->top_level_max_bin_id = max_hibf_id;
+    store.hibf_layout->top_level_max_bin_id = seqan::hibf::layout::hierarchical_binning{store, config}.execute();
 
     // sort records ascending by the number of bin indices (corresponds to the IBF levels)
     // GCOVR_EXCL_START

diff --git a/src/layout/execute.cpp b/src/layout/execute.cpp