Merge branch 'feature-c/2632-ordre-des-locus-mieux-qu-alphabetique' into 'dev'

Resolve "Ordre des locus mieux qu'alphabétique"

Closes #2632

See merge request !393

browser/js/info.js

@@ -332,7 +332,7 @@ Info.prototype = {
         var keys = 0;
 
         var key_list = this.m.system_available;
-        key_list.sort();
+        
 
         var last_key = "";
 

browser/js/model_loader.js

@@ -325,6 +325,8 @@ Model_loader.prototype = {
                 self.system_available.push(system)
             }
         }
+        self.system_available.sort(locus_cmp)
+
         for (var sa in self.system_available){
             system = this.system_available[sa]
             self.system_selected.push(system)

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
@@ -648,3 +648,34 @@ function pearsonCoeff(l1, l2) {
 }
 
 function logadd1(x) { return Math.log(x + 1) ; }
+
+
+
+/**
+ * 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 locus_cmp(valA, valB){
+    // Ordered list of all  generic locus 
+    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 0
+}

browser/test/QUnit/testFiles/info_test.js

@@ -49,8 +49,8 @@ QUnit.test("read details", function(assert) {
 
     m.keep_one_active_system('IGH')
     var sbnm = document.getElementsByClassName('systemBoxNameMenu')
-    assert.includes(sbnm[0].outerHTML, '<span class="systemBoxNameMenu IGH">', 'system box IGH is still active')
-    assert.includes(sbnm[1].outerHTML, '<span class="systemBoxNameMenu inactive TRG">', 'system box TRG is inactive')
+    assert.includes(sbnm[0].outerHTML, '<span class="systemBoxNameMenu inactive TRG">', 'system box TRG is inactive')
+    assert.includes(sbnm[1].outerHTML, '<span class="systemBoxNameMenu IGH">', 'system box IGH is still active')
 
     var reads = document.getElementsByClassName('reads_details')[0]
     assert.includes(reads.outerHTML, 'analyzed reads</span><span>200 (100.00%)', 'read details: analyzed reads (same than before)')

browser/test/QUnit/testFiles/tools_test.js

@@ -393,3 +393,19 @@ QUnit.test("Pearson coefficient", function(assert) {
     assert.equal(pearsonCoeff([3, 2, 1], [10, 20, 30]), -1)
     }
 );
+
+
+QUnit.test("Sort list locus", function(assert) {
+
+    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)
+
+    assert.deepEqual(list_test_1, wait_test_1, "list2 is correctly sorted")
+    assert.deepEqual(list_test_2, wait_test_2, "list2 is correctly sorted")
+    }
+);

browser/test/functional/test_multilocus.rb

@@ -31,7 +31,7 @@ class TestMultilocus < BrowserTest
   end
 
   def test_00_germline
-    assert ($b.div(:id => 'info').span(:class => 'systemBoxNameMenu', :index => 2).text.include? 'TRA'), 'missing system TRA'
+    assert ($b.div(:id => 'info').span(:class => 'systemBoxNameMenu', :index => 0).text.include? 'TRA'), 'missing system TRA'
   end
 
   def test_00_legend_scatterplot