Merge int vectors in temporary chain index

vgteam · Dec 6, 2024 · 84a80f4 · 84a80f4
1 parent 6cff676
commit 84a80f4
Show file tree

Hide file tree

Showing 2 changed files with 16 additions and 13 deletions.
diff --git a/bdsg/include/bdsg/snarl_distance_index.hpp b/bdsg/include/bdsg/snarl_distance_index.hpp
@@ -1527,13 +1527,16 @@ class SnarlDistanceIndex : public SnarlDecomposition, public TriviallySerializab
             bool loopable = true; //If this is a looping snarl, this is false if the last snarl is not start-end connected
 
             vector<pair<temp_record_t, size_t>> children; //All children, both nodes and snarls, in order
+
             //Distances for the chain, one entry per node
-            //TODO This would probably be more efficient as a vector of a struct of five ints
-            vector<size_t> prefix_sum;
-            vector<size_t> max_prefix_sum;
-            vector<size_t> forward_loops;
-            vector<size_t> backward_loops;
-            vector<size_t> chain_components;//Which component does each node belong to, usually all 0s
+            struct chain_distances_t {
+                size_t prefix_sum;
+                size_t max_prefix_sum;
+                size_t forward_loop;
+                size_t backward_loop;
+                size_t chain_component;//Which component does each node belong to, usually all 0s
+            };
+            vector<chain_distances_t> per_node_distances;
 
             size_t get_max_record_length(bool include_distances) const;
         };

diff --git a/bdsg/src/snarl_distance_index.cpp b/bdsg/src/snarl_distance_index.cpp
@@ -6164,14 +6164,14 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
 
                     ChainRecordWriter chain_record_constructor;
 
-                    if (temp_chain_record.chain_components.back() == 0 || ignore_distances) {
+                    if (temp_chain_record.per_node_distances.back().chain_component == 0 || ignore_distances) {
                         record_t record_type = ignore_distances ? CHAIN : DISTANCED_CHAIN;
                         chain_record_constructor = ChainRecordWriter(snarl_tree_records->size(), record_type,
-                                                               temp_chain_record.prefix_sum.size(), &snarl_tree_records);
+                                                               temp_chain_record.per_node_distances.size(), &snarl_tree_records);
                         chain_record_constructor.set_start_end_connected();
                     } else {
                         chain_record_constructor = ChainRecordWriter(snarl_tree_records->size(), MULTICOMPONENT_CHAIN,
-                                                               temp_chain_record.prefix_sum.size(), &snarl_tree_records);
+                                                               temp_chain_record.per_node_distances.size(), &snarl_tree_records);
                     }
                     chain_record_constructor.set_parent_record_offset(
                             record_to_offset[make_pair(temp_index_i, temp_chain_record.parent)]);
@@ -6231,15 +6231,15 @@ void SnarlDistanceIndex::get_snarl_tree_records(const vector<const TemporaryDist
                                 //Make a new node record
                                 size_t new_offset = chain_record_constructor.add_node(
                                         temp_node_record.node_id, temp_node_record.node_length, temp_node_record.reversed_in_parent,
-                                        temp_chain_record.prefix_sum[chain_node_i], temp_chain_record.forward_loops[chain_node_i],
-                                        temp_chain_record.backward_loops[chain_node_i], temp_chain_record.chain_components[chain_node_i],
-                                        temp_chain_record.max_prefix_sum[chain_node_i],
+                                        temp_chain_record.per_node_distances[chain_node_i].prefix_sum, temp_chain_record.per_node_distances[chain_node_i].forward_loop,
+                                        temp_chain_record.per_node_distances[chain_node_i].backward_loop, temp_chain_record.per_node_distances[chain_node_i].chain_component,
+                                        temp_chain_record.per_node_distances[chain_node_i].max_prefix_sum,
                                         last_child_offset.first, last_child_was_nontrivial_snarl,
                                         !ignore_distances);
 
                                 //Remember this node as the last thing in the chain
                                 last_child_offset = make_pair(new_offset, false);
-                                if (temp_chain_record.forward_loops[chain_node_i] == 0) {
+                                if (temp_chain_record.per_node_distances[chain_node_i].forward_loop == 0) {
                                     last_child_was_nontrivial_snarl = true;
                                 } else {
                                     last_child_was_nontrivial_snarl = false;