Speed improvements

src/hiv_tx_network.js

@@ -799,7 +799,8 @@ class HIVTxNetwork {
     filter,
     no_clone,
     given_json,
-    include_extra_edges
+    include_extra_edges,
+    edge_subset
   ) {
     var cluster_json = {};
     var map_to_id = {};
@@ -818,17 +819,20 @@ class HIVTxNetwork {
 
     given_json = given_json || this.json;
 
-    cluster_json.Edges = _.filter(given_json.Edges, (e) => {
-      if (_.isUndefined(e.source) || _.isUndefined(e.target)) {
-        return false;
-      }
+    cluster_json.Edges = _.filter(
+      edge_subset ? edge_subset : given_json.Edges,
+      (e) => {
+        if (_.isUndefined(e.source) || _.isUndefined(e.target)) {
+          return false;
+        }
 
-      return (
-        given_json.Nodes[e.source].id in map_to_id &&
-        given_json.Nodes[e.target].id in map_to_id &&
-        (include_extra_edges || !HIVTxNetwork.is_edge_injected(e))
-      );
-    });
+        return (
+          given_json.Nodes[e.source].id in map_to_id &&
+          given_json.Nodes[e.target].id in map_to_id &&
+          (include_extra_edges || !HIVTxNetwork.is_edge_injected(e))
+        );
+      }
+    );
 
     if (filter) {
       cluster_json.Edges = _.filter(cluster_json.Edges, filter);
@@ -1269,6 +1273,9 @@ class HIVTxNetwork {
         this.node_id_to_object[n.id] = n;
         nodeID2idx[n.id] = i;
       });
+
+      let traversal_cache = null;
+
       _.each(groups, (pg) => {
         if (!pg.validated) {
           pg.node_objects = [];
@@ -1318,17 +1325,35 @@ class HIVTxNetwork {
 
           /** all the network nodes connected to the nodes in the CoI at 1.5%; directly or indirectly*/
 
+          if (!traversal_cache) {
+            traversal_cache = [
+              misc.hivtrace_compute_adjacency_with_edges(
+                this.json["Nodes"],
+                this.json["Edges"],
+                (e) => e.length <= 0.015
+              ),
+              misc.hivtrace_compute_adjacency_with_edges(
+                this.json["Nodes"],
+                this.json["Edges"],
+                (e) => e.length <= this.subcluster_threshold
+              ),
+            ];
+          }
+
+          let saved_traversal_edges = [];
           const node_set15 = _.flatten(
             misc.hivtrace_cluster_depthwise_traversal(
               this.json["Nodes"],
               this.json["Edges"],
               (e) => e.length <= 0.015,
+              saved_traversal_edges,
+              pg.node_objects,
               null,
-              pg.node_objects
+              traversal_cache[0]
             )
           );
 
-          const saved_traversal_edges = auto_extend ? [] : null;
+          let saved_traversal_edges_sub = [];
 
           /** all the network nodes connected to the nodes in the subcluster threshold (0.5%);
               also saves all the edges that have been taken if auto_extend is true  */
@@ -1338,11 +1363,15 @@ class HIVTxNetwork {
               this.json["Nodes"],
               this.json["Edges"],
               (e) => e.length <= this.subcluster_threshold,
-              saved_traversal_edges,
-              pg.node_objects
+              saved_traversal_edges_sub,
+              pg.node_objects,
+              null,
+              traversal_cache[1]
             )
           );
 
+          //console.log (saved_traversal_edges)
+
           const direct_at_15 = new Set();
 
           /** all the network nodes connected to the nodes in the CoI at 1.5%; only directly */
@@ -1354,7 +1383,8 @@ class HIVTxNetwork {
               (my_nodeset.has(this.json["Nodes"][e.target].id) ||
                 my_nodeset.has(this.json["Nodes"][e.source].id)),
             //null,
-            true
+            true,
+            saved_traversal_edges
           );
 
           /** all the network nodes connected to the nodes in the CoI at 1.5%; only directly */
@@ -1376,7 +1406,8 @@ class HIVTxNetwork {
               e.length <= this.subcluster_threshold &&
               (my_nodeset.has(this.json["Nodes"][e.target].id) ||
                 my_nodeset.has(this.json["Nodes"][e.source].id)),
-            true
+            true,
+            saved_traversal_edges_sub
           );
 
           const direct_subcluster = new Set();

src/misc.js

@@ -598,6 +598,44 @@ function hivtrace_compute_adjacency(nodes, edges, edge_filter) {
   return adjacency;
 }
 
+/**
+ * Performs a depth-wise traversal on a cluster of nodes, considering edges and optional filters.
+ *
+ * @param {Object[]} nodes - An array of node objects. Each node should have an `id` property.
+ * @param {Object[]} edges - An array of edge objects. Each edge should have `source` and `target` properties
+ *   referencing node IDs.
+ * @param {Function} [edge_filter] - An optional filtering function applied to edges before traversal.
+ *   The function should accept an edge object and return a boolean indicating whether to include the edge.
+
+    computes and returns an adjacency list in the form
+    
+    node id => set of adjacent (connected) node ids
+    
+
+*/
+
+function hivtrace_compute_adjacency_with_edges(nodes, edges, edge_filter) {
+  let adjacency = {};
+
+  _.each(edges, (e) => {
+    if (!edge_filter || edge_filter(e)) {
+      let src = nodes[e.source];
+      let tgt = nodes[e.target];
+
+      if (!(src.id in adjacency)) {
+        adjacency[src.id] = [];
+      }
+      adjacency[src.id].push([tgt, e]);
+
+      if (!(tgt.id in adjacency)) {
+        adjacency[tgt.id] = [];
+      }
+      adjacency[tgt.id].push([src, e]);
+    }
+  });
+  return adjacency;
+}
+
 /**
  * Performs a depth-wise traversal on a cluster of nodes, considering edges and optional filters.
  *
@@ -623,7 +661,8 @@ function hivtrace_cluster_depthwise_traversal(
   edge_filter,
   save_edges,
   seed_nodes,
-  white_list
+  white_list,
+  given_adjacency
   // an optional set of node IDs (a subset of 'nodes') that will be considered for traversal
   // it is further assumed that seed_nodes are a subset of white_list, if the latter is specified
 ) {
@@ -633,33 +672,44 @@ function hivtrace_cluster_depthwise_traversal(
 
   seed_nodes = seed_nodes || nodes;
 
-  _.each(nodes, (n) => {
-    n.visited = false;
-    adjacency[n.id] = [];
-  });
-
-  if (edge_filter) {
-    edges = _.filter(edges, edge_filter);
-  }
+  if (given_adjacency) {
+    _.each(nodes, (n) => {
+      n.visited = false;
+    });
+    adjacency = given_adjacency;
+  } else {
+    _.each(nodes, (n) => {
+      n.visited = false;
+      adjacency[n.id] = [];
+    });
 
-  if (white_list) {
-    edges = _.filter(
-      edges,
-      (e) =>
-        white_list.has(nodes[e.source].id) && white_list.has(nodes[e.target].id)
-    );
-  }
+    if (edge_filter) {
+      edges = _.filter(edges, edge_filter);
+    }
 
-  _.each(edges, (e) => {
-    try {
-      adjacency[nodes[e.source].id].push([nodes[e.target], e]);
-      adjacency[nodes[e.target].id].push([nodes[e.source], e]);
-    } catch {
-      throw Error(
-        "Edge does not map to an existing node " + e.source + " to " + e.target
+    if (white_list) {
+      edges = _.filter(
+        edges,
+        (e) =>
+          white_list.has(nodes[e.source].id) &&
+          white_list.has(nodes[e.target].id)
       );
     }
-  });
+
+    _.each(edges, (e) => {
+      try {
+        adjacency[nodes[e.source].id].push([nodes[e.target], e]);
+        adjacency[nodes[e.target].id].push([nodes[e.source], e]);
+      } catch {
+        throw Error(
+          "Edge does not map to an existing node " +
+            e.source +
+            " to " +
+            e.target
+        );
+      }
+    });
+  }
 
   var traverse = function (node) {
     if (!(node.id in by_node)) {
@@ -1277,4 +1327,5 @@ module.exports = {
   get_ui_element_selector_by_role,
   hivtrace_cluster_complete_clusters,
   hivtrace_compute_adjacency,
+  hivtrace_compute_adjacency_with_edges,
 };

src/tables.js

@@ -37,6 +37,8 @@ function add_a_sortable_table(
     return;
   }
 
+  container.style("display", "none");
+
   var thead = container.selectAll("thead");
   var tbody = container.selectAll("tbody");
 
@@ -106,6 +108,8 @@ function add_a_sortable_table(
       .select(misc.get_ui_element_selector_by_role("table-count-shown"))
       .text(content.length);
   }
+
+  container.style("display", null);
 }
 
 /**