Merge branch 'feature-c/color-by-cdr3' into 'dev'

Provide a color by CDR3 method

See merge request !309

browser/index.html

@@ -166,6 +166,7 @@
                     <div class="div-menu-selector"><select class="menu-selector" onchange="m.changeColorMethod(this.value)">
                         <option value="Tag">tag</option>
                         <option value="clone">clone</option>
+                        <option value="cdr3">CDR3</option>
                         <option value="V">V/5'</option>
                         <option value="J">J/3'</option>
                         <option value="N">N</option>

browser/js/clone.js

@@ -977,6 +977,8 @@ Clone.prototype = {
             }
         } else if (this.m.colorMethod == 'clone') {
             this.color = colorGeneratorIndex(this.index)
+        } else if (this.m.colorMethod == 'cdr3') {
+            this.color = this.getCDR3Color();
         }else if (this.m.colorMethod == "Tag"){
             this.color =  this.m.tag[this.getTag()].color;
         }else if (this.m.colorMethod == "dbscan"){
@@ -1509,6 +1511,22 @@ Clone.prototype = {
         }
     },
 
+    /**
+     * Deterministically return a color associated with the CDR3 (if any)
+     */
+    getCDR3Color: function() {
+        var junction = this.getSegAASequence('junction');
+        if (junction.length == 0)
+            return '';
+        // Convert CDR3 to int
+        var intcdr3 = 0;
+        junction = junction.toUpperCase();
+        for (var i = 0; i < junction.length; i++) {
+            intcdr3 += (junction.charCodeAt(i)-65) * (Math.pow(26, i));
+        }
+        return colorGeneratorIndex(intcdr3);
+    },
+
     /**
     * Get the number of occurrences of the clone in cloneDB
     * @return {int} res - the number of occurrences, undefined if cloneDB wasn't called

browser/test/QUnit/testFiles/clone_test.js

@@ -388,6 +388,23 @@ QUnit.test("tag / color", function(assert) {
     
 });
 
+QUnit.test("color by CDR3", function(assert) {
+    var m = new Model();
+    m.parseJsonData(json_data);
+    var c1 = new Clone(json_clone1, m, 0);
+    var c2 = new Clone(json_clone2, m, 0);
+    m.initClones();
+    var color = c1.getCDR3Color();
+    c1.seg.junction.aa = "AZERTY";
+    var color2 = c1.getCDR3Color();
+
+    // Actually it could happen that some different CDR3s have the same colours
+    assert.equal(color != color2, true, "two CDR3 should have different"
+                 + " colors");
+
+    assert.equal(c2.getCDR3Color(), '');
+});
+
 QUnit.test("export", function(assert) {
     
     var m = new Model();