Merge branch 'feature-c/3513-export-vers-imgt-et-igblast-avec-sequences-unexpected' into 'dev'

Resolve "Export vers IMGT et IgBlast avec séquences unexpected"

Closes #3513

See merge request !307

browser/js/clone.js

@@ -443,6 +443,24 @@ Clone.prototype = {
         return this.m.clusters[this.index]
     },
 
+    /**
+    * @return {string} locus (at least the locus of the 5' gene)cluster number
+    */
+    getLocus: function () {
+
+        var locus = this.get('germline')
+
+        if (typeof this.m.germline[locus] === "undefined") {
+            var loci = [this.getGene("5").substring(0,3), this.getGene("3").substring(0,3) ]
+            locus = loci[0]
+            if (loci[0] != loci[1]) {
+                console.log("Clone " + this.getName() + "recombines sequences from two separate loci. Using: " + locus)
+            }
+        }
+
+        return locus
+    },
+
     /**
      * compute the clone size ( ratio of all clones clustered ) at a given time
      * @param {integer} time - tracking point (default value : current tracking point)

browser/js/segmenter.js

@@ -818,11 +818,11 @@ Segment.prototype = {
                 
                 if (typeof (c.getSequence()) !== 0){
                     request += ">" + c.index + "#" + c.getName() + "\n" + c.getSequence() + "\n";
-            }else{
+                } else {
                     request += ">" + c.index + "#" + c.getName() + "\n" + c.id + "\n";
                 }
                 if (c.getSize()>max){
-                system=c.get('germline')
+                    system = c.getLocus()
                     max=c.getSize()
                 }
             }
@@ -830,7 +830,9 @@ Segment.prototype = {
                 request += ">" +list[i] + "\n" +this.germline[this.sequence[list[i]].locus][list[i]] + "\n";
             }
         }
-        if (address == 'IMGT') imgtPost(this.m.species, request, system);
+        if (address == 'IMGT') {
+            imgtPost(this.m.species, request, system);
+        } 
         if (address == 'IMGTSeg') {
             imgtPostForSegmenter(this.m.species, request, system, this);
             var change_options = {'l01p01c47' : 'N', // Deactivate default output

browser/test/QUnit/testFiles/clone_test.js

@@ -35,7 +35,7 @@ QUnit.module("Clone", {
         "name" : some_name,
         "reads" : [10,10,30,0] ,
         "top" : 2,
-        "germline" : "TRG",
+        "germline" : "IGH",
         "warn": [{
             "code": "Wxx",
             "msg": "a warning that is only an information",
@@ -139,6 +139,9 @@ QUnit.test("name, informations, getHtmlInfo", function(assert) {
     assert.equal(c2.getName(), some_name, "clone2, .getName()");
     assert.equal(c2.getShortName(), "IGHV3-23 6/ACGTG/4 D1-1 5/12/4 J5*02", "clone2, .getShortName()");
 
+    assert.equal(c1.getLocus(), "TRG")
+    assert.equal(c2.getLocus(), "IGH")
+
     assert.equal(c1.isWarned(), 'warn', "clone1 is warned (client, bad e-value)")
     assert.equal(c2.isWarned(), false, "clone2 is not warned (only 'info')")
     assert.equal(c3.isWarned(), 'warn', "clone3 is warned with 'warn'")