Fix bug sourced from merge

app/js/app-menu.js

@@ -648,33 +648,6 @@ module.exports = function() {
  }
  });
 
- $("#gpml-file-input").change(function () {
-
- var chiseInstance = appUtilities.getActiveChiseInstance();
- var cy = appUtilities.getActiveCy();
- if ($(this).val() != "") {
- var file = this.files[0];
- appUtilities.setFileContent(file.name);
- chiseInstance.loadGpml(file, success = function(data){
- if (cy.elements().length !== 0) {
- promptConfirmationView.render(function () {
- chiseInstance.loadSBGNMLText(data.message, false, file.name, cy);
- });
- }
- else {
- chiseInstance.loadSBGNMLText(data.message, false, file.name, cy);
- }
- },
- error = function(data){
- promptFileConversionErrorView.render(); 
- document.getElementById("file-conversion-error-message").innerText = "Conversion service is not available!";
-
- });
-
- $(this).val("");
- }
- });
-
  $("#simple-af-file-input").change(function () {
  var chiseInstance = appUtilities.getActiveChiseInstance();
 
@@ -818,18 +791,6 @@ module.exports = function() {
  // clear urlParams from scratch
  appUtilities.setScratch(cy, 'urlParams', undefined);
 
-
- // get applyLayout value before map properties are filtered, apply layout
- // isn't really a map property so its not added to sbgnviz 
- // validMapProperties
- const applyLayout = urlParams.applyLayoutOnURL === "true";
- const fromURL = urlParams.url !== undefined;
-
- if (urlParams.compoundPadding) {
- const compoundPadding = urlParams.compoundPadding;
- chiseInstance.setCompoundPadding(Number(compoundPadding));
- }
-
  // filter map properties from the url parameters
 
  // get applyLayout value before map properties are filtered, apply layout
@@ -868,24 +829,6 @@ module.exports = function() {
  appUtilities.applyMapColorScheme(urlParams.mapColorScheme, currentGeneralProperties.mapColorSchemeStyle, appUtilities.colorSchemeInspectorView);
  }
 
- if (fromURL && applyLayout) {
- let currentLayoutProperties = appUtilities.getScratch(cy, 'currentLayoutProperties');
-
- // Below is copied from sbgnviz.graphUtilities.updateGraph
- let preferences = {};
- if(cy.nodes().length > 3000 || cy.edges().length > 3000) {
- preferences.quality = "draft";
- }
- preferences.animate = false;
- preferences.randomize = true;
- preferences = $.extend({}, currentLayoutProperties, preferences);
- layoutPropertiesView.applyLayout(preferences);
- }
-
- if (urlParams.mapColorScheme) {
- appUtilities.applyMapColorScheme(urlParams.mapColorScheme, currentGeneralProperties.mapColorSchemeStyle, appUtilities.colorSchemeInspectorView);
- }
-
  // merge the map properties coming from url into
  // the map properties read from file
  for ( var prop in mapPropsFromUrl ) {