Update fct to be call directly inside a sort call

link to #2632

browser/js/model_loader.js

@@ -325,7 +325,7 @@ Model_loader.prototype = {
                 self.system_available.push(system)
             }
         }
-        self.system_available = sort_list_locus(self.system_available)
+        self.system_available.sort(locus_cmp)
 
         for (var sa in self.system_available){
             system = this.system_available[sa]

browser/js/tools.js

@@ -4,7 +4,7 @@ var INS="insertion";
 var DEL="deletion";
 var END_CODON = "end-codon ";
 var END_CODON_NOT_FIRST = "end-codon-not-first ";
-
+var LOCUS_ORDER = [ "TRA", "TRB", "TRB+", "TRG", "TRD", "TRA+D", "TRD+", "IGH", "IGH+", "IGK", "IGK+", "IGL"]
 /**
  * Get codons from two aligned sequences
  * @pre both sequences are aligned together ref.length == seq.length
@@ -649,37 +649,33 @@ function pearsonCoeff(l1, l2) {
 
 function logadd1(x) { return Math.log(x + 1) ; }
 
+
+
 /**
- * Sort list of available locus.
- * The list is ordered on a preordered list of locus.
- * Locus that are not in this list will be added a supplmeent of this one at the end of it.
- * @param  {Array} key_list List of system available in model, or a list of locus
- * @return {Array}          Ordered list of locus
+ * Compare two locus to sort them.
+ * The list is ordered on a preordered list of locus (LOCUS_ORDER).
+ * By this way, locus that are not in this list will be added at the end of it.
+ * @param  {String} valA One locus value
+ * @param  {String} valB Another locus value to compare
+ * @return {Number}      A number -1 if A before B, else 1
  */
-function sort_list_locus(key_list){
+function locus_cmp(valA, valB){
     // Ordered list of all  generic locus 
-    var generic_locus_1 = [ "TRA", "TRB", "TRB+", "TRG", "TRD", "TRA+D", "TRD+", "IGH", "IGH+", "IGK", "IGK+", "IGL"]
-    var generic_locus_2 = [ "TRA", "TRB", "TRB+", "TRG", "TRD", "TRA+D", "TRD+", "IGH", "IGH+", "IGK", "IGK+", "IGL"]
-
-    var index;
-    for (var i = 0; i < generic_locus_1.length; i++) {
-        // If not present, deletion of result list
-        if (key_list.indexOf(generic_locus_1[i]) == -1) {
-            index = generic_locus_2.indexOf(generic_locus_1[i]);
-            generic_locus_2.splice(index, 1);
-        } else {
-            // else deletion of list given
-            index = key_list.indexOf(generic_locus_1[i]);
-            key_list.splice(index, 1);
-        }
-    }
-    // key_list will only contain locus that are not in generic list of locus
-    // Sort keeped elements
-    key_list.sort()
-    
-    // Add these elements to result list
-    for (var j = 0; j < key_list.length; j++) {
-        generic_locus_2.push( key_list[j] )
+    var index_A = LOCUS_ORDER.indexOf(valA)
+    var index_B = LOCUS_ORDER.indexOf(valB)
+
+    if (index_A == -1 && index_B == -1){
+        // Neither A or B are present in LOCUS_ORDER
+        return valA.localeCompare(valB)
+    } else if (index_A != -1 && index_B == -1){
+        // Only A is present in LOCUS_ORDER
+        return -1
+    } else if (index_A == -1 && index_B != -1){
+        // Only B is present in LOCUS_ORDER
+        return 1
+    } else if (index_A != -1 && index_B != -1){
+        // A & B are present in LOCUS_ORDER
+        return index_A - index_B
     }
-    return generic_locus_2
+    return 0
 }

browser/test/QUnit/testFiles/tools_test.js

@@ -397,19 +397,15 @@ QUnit.test("Pearson coefficient", function(assert) {
 
 QUnit.test("Sort list locus", function(assert) {
 
-    liste_sort_1 = [ "TRA", "TRB", "TRB+", "TRG", "TRD", "TRA+D", "TRD+", "IGH", "IGH+", "IGK", "IGK+", "IGL"]
-    console.log( "sort_list_locus" )
     list_test_1 = [ "TRA", "TRB", "TRG", "TRD", "testlocus", "IGH", "IGK", "IGL"]
     wait_test_1 = [ "TRA", "TRB", "TRG", "TRD", "IGH", "IGK", "IGL", "testlocus"]
     list_test_2 = [ "IGH", "IGH+", "unknow_locus", "IGK+", "IGL", "testlocus", "TRA", "TRB", "TRB+", "TRG", "TRD"]
     wait_test_2 = [ "TRA", "TRB", "TRB+", "TRG", "TRD", "IGH", "IGH+", "IGK+", "IGL", "testlocus", "unknow_locus"]
+    
+    list_test_1.sort(locus_cmp)
+    list_test_2.sort(locus_cmp)
 
-    // console.log( "result_1" )
-    // console.log( sort_list_locus(list_test_1))
-    // console.log( "result_2" )
-    // console.log( sort_list_locus(list_test_2))
-
-    assert.deepEqual(sort_list_locus(list_test_1), wait_test_1, "list1 is correctly sorted")
-    assert.deepEqual(sort_list_locus(list_test_2), wait_test_2, "list2 is correctly sorted")
+    assert.deepEqual(list_test_1, wait_test_1, "list2 is correctly sorted")
+    assert.deepEqual(list_test_2, wait_test_2, "list2 is correctly sorted")
     }
 );