move timers into config.

seqan · Aug 13, 2024 · 411ffc5 · 411ffc5
1 parent 1983ec4
commit 411ffc5
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Showing 4 changed files with 20 additions and 31 deletions.
diff --git a/include/chopper/configuration.hpp b/include/chopper/configuration.hpp
@@ -15,6 +15,7 @@
 
 #include <hibf/cereal/path.hpp> // IWYU pragma: keep
 #include <hibf/config.hpp>
+#include <hibf/misc/timer.hpp>
 
 namespace chopper
 {
@@ -72,6 +73,11 @@ struct configuration
     //!\brief The HIBF config which will be used to compute the layout within the HIBF lib.
     seqan::hibf::config hibf_config;
 
+    mutable seqan::hibf::concurrent_timer compute_sketches_timer{};
+    mutable seqan::hibf::concurrent_timer union_estimation_timer{};
+    mutable seqan::hibf::concurrent_timer rearrangement_timer{};
+    mutable seqan::hibf::concurrent_timer dp_algorithm_timer{};
+
     void read_from(std::istream & stream);
 
     void write_to(std::ostream & stream) const;

diff --git a/include/chopper/layout/execute.hpp b/include/chopper/layout/execute.hpp
@@ -12,17 +12,13 @@
 
 #include <chopper/configuration.hpp>
 
-#include <hibf/misc/timer.hpp>
 #include <hibf/sketch/hyperloglog.hpp>
 
 namespace chopper::layout
 {
 
 int execute(chopper::configuration & config,
             std::vector<std::vector<std::string>> const & filenames,
-            std::vector<seqan::hibf::sketch::hyperloglog> const & sketches,
-            seqan::hibf::concurrent_timer & union_estimation_timer,
-            seqan::hibf::concurrent_timer & rearrangement_timer,
-            seqan::hibf::concurrent_timer & dp_algorithm_timer);
+            std::vector<seqan::hibf::sketch::hyperloglog> const & sketches);
 
 } // namespace chopper::layout
diff --git a/src/chopper.cpp b/src/chopper.cpp
@@ -58,11 +58,6 @@ int main(int argc, char const * argv[])
 
     std::vector<seqan::hibf::sketch::hyperloglog> sketches;
 
-    seqan::hibf::concurrent_timer compute_sketches_timer{};
-    seqan::hibf::concurrent_timer union_estimation_timer{};
-    seqan::hibf::concurrent_timer rearrangement_timer{};
-    seqan::hibf::concurrent_timer dp_algorithm_timer{};
-
     try
     {
         if (filenames.empty())
@@ -75,16 +70,11 @@ int main(int argc, char const * argv[])
             chopper::input_functor{filenames, config.precomputed_files, config.k, config.window_size};
         config.hibf_config.number_of_user_bins = filenames.size();
 
-        compute_sketches_timer.start();
+        config.compute_sketches_timer.start();
         seqan::hibf::sketch::compute_sketches(config.hibf_config, sketches);
-        compute_sketches_timer.stop();
-
-        exit_code |= chopper::layout::execute(config,
-                                              filenames,
-                                              sketches,
-                                              union_estimation_timer,
-                                              rearrangement_timer,
-                                              dp_algorithm_timer);
+        config.compute_sketches_timer.stop();
+
+        exit_code |= chopper::layout::execute(config, filenames, sketches);
     }
     catch (std::exception const & ext)
     {
@@ -110,10 +100,10 @@ int main(int argc, char const * argv[])
                       << "layouting_in_seconds\t"
                       << "union_estimation_in_seconds\t"
                       << "rearrangement_in_seconds\n";
-        output_stream << compute_sketches_timer.in_seconds() << '\t';
-        output_stream << dp_algorithm_timer.in_seconds() << '\t';
-        output_stream << union_estimation_timer.in_seconds() << '\t';
-        output_stream << rearrangement_timer.in_seconds() << '\t';
+        output_stream << config.compute_sketches_timer.in_seconds() << '\t';
+        output_stream << config.dp_algorithm_timer.in_seconds() << '\t';
+        output_stream << config.union_estimation_timer.in_seconds() << '\t';
+        output_stream << config.rearrangement_timer.in_seconds() << '\t';
     }
 
     return exit_code;

diff --git a/src/layout/execute.cpp b/src/layout/execute.cpp
@@ -35,10 +35,7 @@ namespace chopper::layout
 
 int execute(chopper::configuration & config,
             std::vector<std::vector<std::string>> const & filenames,
-            std::vector<seqan::hibf::sketch::hyperloglog> const & sketches,
-            seqan::hibf::concurrent_timer & union_estimation_timer,
-            seqan::hibf::concurrent_timer & rearrangement_timer,
-            seqan::hibf::concurrent_timer & dp_algorithm_timer)
+            std::vector<seqan::hibf::sketch::hyperloglog> const & sketches)
 {
     assert(config.hibf_config.number_of_user_bins > 0);
 
@@ -74,14 +71,14 @@ int execute(chopper::configuration & config,
     }
     else
     {
-        dp_algorithm_timer.start();
+        config.dp_algorithm_timer.start();
         hibf_layout = seqan::hibf::layout::compute_layout(config.hibf_config,
                                                           kmer_counts,
                                                           sketches,
                                                           seqan::hibf::iota_vector(sketches.size()),
-                                                          union_estimation_timer,
-                                                          rearrangement_timer);
-        dp_algorithm_timer.stop();
+                                                          config.union_estimation_timer,
+                                                          config.rearrangement_timer);
+        config.dp_algorithm_timer.stop();
 
         if (config.output_verbose_statistics)
         {