From 8b7e3fc4eb8f942c2e70543fa42594f5c094c925 Mon Sep 17 00:00:00 2001
From: Gopi Gugan <gopi.gugan@gmail.com>
Date: Tue, 11 Oct 2022 12:49:16 -0400
Subject: [PATCH 1/2] Restore search, display recombinants during search

---
 js/covizu.js   | 5 +++--
 js/drawtree.js | 2 +-
 js/search.js   | 5 +++++
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/js/covizu.js b/js/covizu.js
index 68b4129..6784c89 100644
--- a/js/covizu.js
+++ b/js/covizu.js
@@ -195,8 +195,9 @@ req.done(async function() {
   curr_date.setFullYear(curr_date.getFullYear() - 1);
 
   // Maps id to a cidx
-  for (i in tips) {
-    id_to_cidx[i] = 'cidx-' + tips[i].cluster_idx
+  var all_tips = [...recombinant_tips, ...tips]
+  for (i in all_tips) {
+    id_to_cidx[i] = 'cidx-' + all_tips[i].cluster_idx
   }
 
   // Maps cidx to an id
diff --git a/js/drawtree.js b/js/drawtree.js
index 19fa696..64d5d24 100644
--- a/js/drawtree.js
+++ b/js/drawtree.js
@@ -319,7 +319,7 @@ function draw_clusters(tips, recombinant_tips, redraw=false) {
     .attr("height", 10)
     .attr("class", "default recombinant")
     .attr("cidx", function(d) { return "cidx-" + d.cluster_idx; })
-    .attr("id", function(d, i) { return "id-" + i; })
+    .attr("id", function(d, i) { return "id-" + map_cidx_to_id['cidx-' + d.cluster_idx]; })
     .on('mouseover', mouseover)
     .on("mouseout", function() {
       d3.select(this)
diff --git a/js/search.js b/js/search.js
index 0bb080b..1f62cbc 100644
--- a/js/search.js
+++ b/js/search.js
@@ -73,6 +73,11 @@ async function wrap_search() {
     return;
   }
 
+  // Display recombinants when doing a search
+  $('#display-option').attr('checked', 'checked');
+  $(".recombinant-tree-content").show()
+  $(".recombtitle").show()
+
   var start_date, end_date;
   if (start_date_text === "") {
     start_date = utcDate("2020-01-01");

From 80a16f788cee0d0b36c38d6e9d761c0e60fad25d Mon Sep 17 00:00:00 2001
From: bonnielu <bonnielu2002@gmail.com>
Date: Tue, 11 Oct 2022 14:29:57 -0400
Subject: [PATCH 2/2] fix for #428

---
 js/drawtree.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/js/drawtree.js b/js/drawtree.js
index 64d5d24..1c38172 100644
--- a/js/drawtree.js
+++ b/js/drawtree.js
@@ -106,7 +106,7 @@ function draw_cluster_box(rect) {
  * Draw time-scaled tree in SVG
  * @param {Array} df:  data frame
  */
-function drawtree(df, redraw=true) {
+function drawtree(df, org_df, redraw=true) {
 
   // Sets margin top to align vertical scrollbar with the time-scaled tree
   $('#tree-vscroll').css('margin-top', document.getElementById("tree-title").clientHeight + document.getElementById("svg-timetreeaxis").clientHeight + $('#inner-hscroll').height() + 5);
@@ -123,8 +123,8 @@ function drawtree(df, redraw=true) {
   // adjust d3 scales to data frame
   if(!redraw) {
     xScale.domain([
-      d3.min(df, xValue)-0.05, 
-      date_to_xaxis(d3.max(df, function(d) {return d.last_date})) 
+      d3.min(org_df, xValue)-0.05, 
+      date_to_xaxis(d3.max(org_df, function(d) {return d.last_date})) 
     ]);
   }
 
@@ -885,7 +885,7 @@ async function redraw_tree(cutoff_date, redraw=true) {
 
   document.querySelector("#svg-timetree > svg").innerHTML = ''; 
   document.querySelector("#svg-recombinants > svg").innerHTML = '';
-  drawtree(final_df, redraw=redraw);
+  drawtree(final_df, df_copy, redraw=redraw);
   draw_clusters(filtered_tips, filtered_recomb_tips, redraw);
 
   if(redraw) {