germline_builder.js : convert(again) germlines.data from json to js / and add...

germline_builder.js : convert(again) germlines.data from json to js /  and add fallback for offline mode

browser/index.html

@@ -51,6 +51,7 @@
         <script type="text/javascript" src='js/menu.js'></script>
         <script type="text/javascript" src='js/dbscan.js'></script>
         <script type="text/javascript" src='js/germline.js'></script>
+        <script type="text/javascript" src='../germline/germlines.data'></script>
         <script type="text/javascript" src='js/germline_builder.js'></script>
         <script type="text/javascript" src='js/segmenter.js'></script>
         <script type="text/javascript" src='js/model.js'></script>

browser/js/builder.js

@@ -677,7 +677,7 @@ Builder.prototype = {
         span.className = "systemBox";
         if ((typeof system != 'undefined')){
             span.appendChild(document.createTextNode(this.m.germlineList.getShortcut(system)));
-            if (this.m.system_selected.indexOf(system) == -1) 
+            if (this.m.system_selected.indexOf(system) != -1) 
                 span.style.background = this.m.germlineList.getColor(system)
             span.title = system
         }else{

browser/js/germline_builder.js

@@ -18,8 +18,8 @@
  */
 
 function GermlineList () {
-    this.init()
     this.list = {}
+    this.init()
 }
 
 GermlineList.prototype = {
@@ -30,7 +30,7 @@ GermlineList.prototype = {
     
     //load germlines.data file from server
     load : function () {
-        var self=this;
+        this.fallbackLoad() //just in case
         
         $.ajax({
             url: window.location.origin + "/germline/germlines.data",
@@ -39,19 +39,25 @@ GermlineList.prototype = {
                     //remove comment (json don't have comment)
                     var json = result.replace(/ *\/\/[^\n]*\n */g , "")
                     //convert from js to json (json begin with { or [, never with a var name)
-                    json = json.replace("germlines = " , "")
+                    json = json.replace("germline_data = " , "")
                     self.list = jQuery.parseJSON(json);
                 }
                 catch(err){
-                    myConsole.flash("server : germlines.data malformed", 2);
+                    myConsole.flash("server : germlines.data malformed, use local js file instead (can be outdated) ", 2);
+                    
                 }
             },
             error: function (request, status, error) {
-                myConsole.flash("server : error impossible to retrieve germlines.data", 2);
+                myConsole.flash("server : error impossible to retrieve germlines.data, use local js file instead (can be outdated)", 2);
             },
             dataType: "text"
         });
         
+        
+    },
+    
+    fallbackLoad : function () {
+        this.list = germline_data
     },
     
     //add a list of custom germlines

browser/js/graph.js

@@ -958,7 +958,7 @@ Graph.prototype = {
                 }
             })
             .attr("class", function (p) {
-                if (!p.active()){
+                if (!p.active){
                     return "graph_inactive";
                 }else{
                     return "graph_data";

germline/germlines.data

-{
+germline_data = {
     
     "TRA": {
         "shortcut": "A",