From 0618da197b740ee3b92a7f260555109171e8706c Mon Sep 17 00:00:00 2001
From: Sergei <spond@temple.edu>
Date: Sat, 2 Nov 2024 09:40:12 -0400
Subject: [PATCH] Adjusting some of the network statistics to be aware of MSPP

---
 html/priority-sets-args.html       |  2 +-
 src/clusternetwork.js              | 15 +++++++++++++++
 src/hivtraceClusterGraphSummary.js |  6 +++---
 3 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/html/priority-sets-args.html b/html/priority-sets-args.html
index 6df0019..52be824 100644
--- a/html/priority-sets-args.html
+++ b/html/priority-sets-args.html
@@ -975,7 +975,7 @@ <h5 class="modal-desc">Select CoI from the list</h5>
           } else {
             d3.select("#app-error").style("display", "none");
             hivtrace.histogramDistances(graph, histogram_tag, histogram_label);
-            hivtrace.graphSummary(graph, graph_summary_tag);
+            hivtrace.graphSummary(user_graph.json, graph_summary_tag);
 
             [
               "#main-tab",
diff --git a/src/clusternetwork.js b/src/clusternetwork.js
index 117c837..fb074df 100755
--- a/src/clusternetwork.js
+++ b/src/clusternetwork.js
@@ -1711,12 +1711,15 @@ var hivtrace_cluster_network_graph = function (
     self.cluster_sizes = [];
     self.cluster_sizes_in_entities = {};
 
+    let cluster_set = new Set();
+
     graph_data.Nodes.forEach((d) => {
       if (typeof self.cluster_sizes[d.cluster - 1] === "undefined") {
         self.cluster_sizes[d.cluster - 1] = 1;
       } else {
         self.cluster_sizes[d.cluster - 1]++;
       }
+      cluster_set.add(d.cluster);
       if ("is_lanl" in d) {
         d.is_lanl = d.is_lanl === "true";
       }
@@ -1732,13 +1735,25 @@ var hivtrace_cluster_network_graph = function (
     });
 
     if (self.has_multiple_sequences) {
+      let entity_count = 0;
       self.apply_to_entities((entity_id, nodes) => {
         if (self.cluster_sizes_in_entities[nodes[0].cluster]) {
           self.cluster_sizes_in_entities[nodes[0].cluster]++;
         } else {
           self.cluster_sizes_in_entities[nodes[0].cluster] = 1;
         }
+        entity_count++;
+      });
+      self.json["Network Summary"]["Nodes"] = entity_count;
+      self.json["Network Summary"]["Clusters"] = _.size(
+        self.cluster_sizes_in_entities
+      );
+      self.json["Cluster sizes"] = [];
+      _.each(self.cluster_sizes_in_entities, (d, c) => {
+        self.json["Cluster sizes"].push(d);
       });
+    } else {
+      self.json["Network Summary"]["Clusters"] = cluster_set.size;
     }
 
     /* add buttons and handlers */
diff --git a/src/hivtraceClusterGraphSummary.js b/src/hivtraceClusterGraphSummary.js
index 8859afa..99d8fc8 100644
--- a/src/hivtraceClusterGraphSummary.js
+++ b/src/hivtraceClusterGraphSummary.js
@@ -37,7 +37,7 @@ function hivtraceClusterGraphSummary(graph, tag, not_CDC) {
   if (!summary_table.empty()) {
     _.each(graph["Network Summary"], (value, key) => {
       // Handle special case for cluster count
-      if (key === "Clusters") {
+      if (not_CDC && key === "Clusters") {
         value = _.size(graph["Cluster description"]);
       }
 
@@ -97,7 +97,7 @@ function hivtraceClusterGraphSummary(graph, tag, not_CDC) {
     degrees["min"] + " - " + degrees["max"],
   ]);
   table_data.push([
-    "&nbsp;&nbsp;<i>" + __("statistics")["interquartile_range"] + "range</i>",
+    "&nbsp;&nbsp;<i>" + __("statistics")["interquartile_range"] + "</i>",
     degrees["Q1"] + " - " + degrees["Q3"],
   ]);
 
@@ -123,7 +123,7 @@ function hivtraceClusterGraphSummary(graph, tag, not_CDC) {
         _defaultPercentFormat(degrees["max"]),
     ]);
     table_data.push([
-      "&nbsp;&nbsp;<i>" + __("statistics")["interquartile_range"] + "range</i>",
+      "&nbsp;&nbsp;<i>" + __("statistics")["interquartile_range"] + "</i>",
       _defaultPercentFormat(degrees["Q1"]) +
         " - " +
         _defaultPercentFormat(degrees["Q3"]),