From 9a0200875867e9f63414a94f6f32c66d0d7085be Mon Sep 17 00:00:00 2001
From: Salih Altun <muhammedsalihaltun@gmail.com>
Date: Thu, 8 Apr 2021 14:22:08 +0300
Subject: [PATCH] File conversion changes

  Take URL parameters into account from Newt.
---
 src/utilities/file-utilities-factory.js           |  9 +++++----
 src/utilities/main-utilities-factory.js           |  4 ++--
 src/utilities/nwt-to-json-converter-factory.js    |  4 ++--
 src/utilities/sbgnml-to-json-converter-factory.js | 10 +++++++---
 4 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/src/utilities/file-utilities-factory.js b/src/utilities/file-utilities-factory.js
index 42e1d024..eeda7866 100644
--- a/src/utilities/file-utilities-factory.js
+++ b/src/utilities/file-utilities-factory.js
@@ -215,9 +215,9 @@ module.exports = function () {
    fileUtilities.loadFile( file, convert, callback1, callback2, fileUtilities.collapseMarkedNodes );
  };
 
- fileUtilities.loadNwtFile = function(file, callback1, callback2) {
+ fileUtilities.loadNwtFile = function(file, callback1, callback2, urlParams) {
    var convert = function( text ) {
-     return nwtToJson.convert(textToXmlObject(text));
+     return nwtToJson.convert(textToXmlObject(text), urlParams);
    };
 
    fileUtilities.loadFile( file, convert, callback1, callback2, fileUtilities.collapseMarkedNodes );
@@ -314,9 +314,10 @@ module.exports = function () {
    reader.readAsText(file);
  };
 
- fileUtilities.loadSBGNMLText = function(textData, tileInfoBoxes){
+ fileUtilities.loadSBGNMLText = function(textData, tileInfoBoxes, filename, cy, urlParams){
      setTimeout(function () {
-         updateGraph(sbgnmlToJson.convert(textToXmlObject(textData)), undefined, undefined, tileInfoBoxes);
+         updateGraph(sbgnmlToJson.convert(textToXmlObject(textData), urlParams), undefined, undefined, tileInfoBoxes);
+         $(document).trigger("sbgnvizLoadFileEnd", [filename, cy]);
          uiUtilities.endSpinner("load-file-spinner");
      }, 0);
 
diff --git a/src/utilities/main-utilities-factory.js b/src/utilities/main-utilities-factory.js
index a3c769c3..37b8f7f3 100644
--- a/src/utilities/main-utilities-factory.js
+++ b/src/utilities/main-utilities-factory.js
@@ -567,8 +567,8 @@ module.exports = function () {
 
   // Converts given sbgnml data to a json object in a special format
   // (http://js.cytoscape.org/#notation/elements-json) and returns it.
-  mainUtilities.convertSbgnmlToJson = function(data) {
-    return sbgnmlToJson.convert(data);
+  mainUtilities.convertSbgnmlToJson = function(data, urlParams) {
+    return sbgnmlToJson.convert(data, urlParams);
   };
 
   mainUtilities.convertNwtToJson = function(data) {
diff --git a/src/utilities/nwt-to-json-converter-factory.js b/src/utilities/nwt-to-json-converter-factory.js
index bc692bdb..b4d9f6aa 100644
--- a/src/utilities/nwt-to-json-converter-factory.js
+++ b/src/utilities/nwt-to-json-converter-factory.js
@@ -140,8 +140,8 @@ module.exports = function() {
     } );
   }
 
-  nwtToJson.convert = function(xmlObject) {
-    var graphData = sbgnmlToJson.convert(xmlObject);
+  nwtToJson.convert = function(xmlObject, urlParams) {
+    var graphData = sbgnmlToJson.convert(xmlObject, urlParams);
     var mapType = elementUtilities.mapType;
 
     if (mapType !== 'PD' && mapType !== 'AF' && elementUtilities.mapType !== 'HybridSbgn') {
diff --git a/src/utilities/sbgnml-to-json-converter-factory.js b/src/utilities/sbgnml-to-json-converter-factory.js
index 22aba8da..27380848 100644
--- a/src/utilities/sbgnml-to-json-converter-factory.js
+++ b/src/utilities/sbgnml-to-json-converter-factory.js
@@ -1073,7 +1073,7 @@ module.exports = function () {
     
   };
 
-  sbgnmlToJson.convert = function (xmlObject) {
+  sbgnmlToJson.convert = function (xmlObject, urlParams) {
     var self = this;
     var cytoscapeJsNodes = [];
     var cytoscapeJsEdges = [];
@@ -1129,8 +1129,12 @@ module.exports = function () {
       }
     }
     
-    var minDistanceToChildren = Number.MAX_SAFE_INTEGER ;
-    if (!map.extension) {
+    var minDistanceToChildren = Number.MAX_SAFE_INTEGER;
+
+    if(urlParams && urlParams.compoundPadding) {
+      mainUtilities.setCompoundPadding(Number(urlParams.compoundPadding)); 
+    }
+    else if (!map.extension) {
       for (var i = 0; i < glyphs.length; i++) {
         var glyph = glyphs[i];
        // if(glyph.class_ == "complex")continue;