refactor: reduce cognitive complexity #220

GenSpectrum · Jan 19, 2024 · 5404a6d · 5404a6d
1 parent 77eb32d
commit 5404a6d
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Showing 2 changed files with 27 additions and 15 deletions.
diff --git a/include/silo/storage/sequence_store.h b/include/silo/storage/sequence_store.h
@@ -76,6 +76,11 @@ class SequenceStorePartition {
 
    void fillIndexes(const vector<optional<string>>& genomes);
 
+   void addSymbolsToPositions(
+      const size_t& position,
+      SymbolMap<SymbolType, vector<uint32_t>>& ids_per_symbol_for_current_position
+   );
+
    void fillNBitmaps(const vector<optional<string>>& genomes);
 
   public:

diff --git a/src/silo/storage/sequence_store.cpp b/src/silo/storage/sequence_store.cpp
@@ -171,25 +171,33 @@ void SequenceStorePartition<SymbolType>::fillIndexes(const vector<optional<strin
                   );
                }
             }
-            for (const auto& symbol : SymbolType::SYMBOLS) {
-               if (!ids_per_symbol_for_current_position.at(symbol).empty()) {
-                  positions[position].bitmaps[symbol].addMany(
-                     ids_per_symbol_for_current_position.at(symbol).size(),
-                     ids_per_symbol_for_current_position.at(symbol).data()
-                  );
-                  ids_per_symbol_for_current_position[symbol].clear();
-               }
-               if (symbol == positions[position].symbol_whose_bitmap_is_flipped) {
-                  positions[position].bitmaps[symbol].flip(
-                     sequence_count, sequence_count + number_of_sequences
-                  );
-               }
-            }
+            addSymbolsToPositions(position, ids_per_symbol_for_current_position);
          }
       }
    );
 }
 
+template <typename SymbolType>
+void SequenceStorePartition<SymbolType>::addSymbolsToPositions(
+   const size_t& position,
+   SymbolMap<SymbolType, vector<uint32_t>>& ids_per_symbol_for_current_position
+) {
+   for (const auto& symbol : SymbolType::SYMBOLS) {
+      if (!ids_per_symbol_for_current_position.at(symbol).empty()) {
+         positions[position].bitmaps[symbol].addMany(
+            ids_per_symbol_for_current_position.at(symbol).size(),
+            ids_per_symbol_for_current_position.at(symbol).data()
+         );
+         ids_per_symbol_for_current_position[symbol].clear();
+      }
+      if (symbol == positions[position].symbol_whose_bitmap_is_flipped) {
+         positions[position].bitmaps[symbol].flip(
+            sequence_count, sequence_count + positions.size()
+         );
+      }
+   }
+}
+
 template <typename SymbolType>
 void SequenceStorePartition<SymbolType>::fillNBitmaps(const vector<optional<string>>& genomes) {
    const size_t genome_length = positions.size();
@@ -198,7 +206,6 @@ void SequenceStorePartition<SymbolType>::fillNBitmaps(const vector<optional<stri
 
    const tbb::blocked_range<size_t> range(0, genomes.size());
    tbb::parallel_for(range, [&](const decltype(range)& local) {
-      // For every symbol, calculate all sequence IDs that have that symbol at that position
       vector<uint32_t> positions_with_symbol_missing;
       for (size_t sequence_index = local.begin(); sequence_index != local.end(); ++sequence_index) {
          const auto& maybe_genome = genomes[sequence_index];