From 419f804c48132be717775f366a72bc7dcde2efcc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Umut=20Utku=20ER=C5=9EAH=C4=B0NCE?=
 <ersahinceumut@gmail.com>
Date: Tue, 2 Jul 2024 10:47:20 +0300
Subject: [PATCH] uri disconnected nodes

---
 app/js/backbone-views.js |  6 +++++-
 index.html               | 10 +++++++++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/app/js/backbone-views.js b/app/js/backbone-views.js
index 3a28bff9..4f027948 100644
--- a/app/js/backbone-views.js
+++ b/app/js/backbone-views.js
@@ -3026,6 +3026,9 @@ var PathsByURIQueryView = Backbone.View.extend({
           "query-pathsbyURI-URI"
         ).value;
         var uri = self.currentQueryParameters.URI.trim();
+        var removeDisconnected =  document.getElementById(
+          "query-pathsbyURI-checkbox"
+        ).checked;
 
         if (uri.length === 0) {
           document.getElementById("query-pathsbyURI-URI").focus();
@@ -3081,7 +3084,8 @@ var PathsByURIQueryView = Backbone.View.extend({
                   );
                   currentGeneralProperties.inferNestingOnLoad =
                     currentInferNestingOnLoad;
-                  appUtilities.removeDisconnectedNodesAfterQuery([]);
+                  if(removeDisconnected)
+                    appUtilities.removeDisconnectedNodesAfterQuery([]);
                   $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]);
                 } else {
                   new PromptEmptyQueryResultView({
diff --git a/index.html b/index.html
index 90230be6..1f76f7dd 100644
--- a/index.html
+++ b/index.html
@@ -3800,9 +3800,17 @@ <h4 class="modal-title">Paths By URI</h4>
                       </tr>
 
                       <tr>
-                          <td>Enter URI of a pathway</td>
+                          <td class="caption-style-text">Enter URI of a pathway</td>
                           <td style="padding: 10px;"><input id="query-pathsbyURI-URI" type="text"  style="width: 300px;" value= <%= URI %> > </td>
                       </tr>
+                      <tr>
+                        <td colspan=2>
+                          <div style="display: flex; flex-direction: row; column-gap: 5px;">
+                            <div class="caption-style-text">Remove Disconnected Nodes:</div>
+                            <input id="query-pathsbyURI-checkbox" type="checkbox" class="layout-text" style="margin: 0 0;" checked>
+                          </div>
+                        </td>
+                      </tr>
                       </tbody>
                   </table>
               </div>