tools.js: Function to get the common name of a species

IMGT/V-QUEST now requires to have the common name of the species, not the latin one.
Thus we need a function to do the conversion.

See #3913

browser/js/crossDomain.js

@@ -12,7 +12,7 @@ function setCrossDomainModel(model) {
 //parametre IMGT par defaut
 function initImgtInput(species) {
     var imgtInput = {};
-    imgtInput.species = species;
+    imgtInput.species = getSpeciesCommonName(species);
     imgtInput.receptorOrLocusType = "TR";
     imgtInput.inputType = "inline";
     imgtInput.resultType = "synthesis";

browser/js/tools.js

@@ -134,6 +134,25 @@ function get_mutations(ref, seq, frame, with_end_codon) {
     return mutations;
 }
 
+/**
+ * @return the common name of a species. Or the original name if the common
+ * name has not been set. The common names are given so that they are
+ * compatible with IMGT/V-QUEST®
+ */
+function getSpeciesCommonName(species) {
+    var lower_species = species.toLowerCase();
+    switch(lower_species) {
+    case "homo sapiens":
+        return "human";
+    case "mus musculus":
+        return "house mouse";
+    case "gallus gallus":
+        return "chicken";
+    default:
+        return species;
+    }
+}
+
 /**
  * Find the position of the nth occurence of needle
  *

browser/test/QUnit/testFiles/tools_test.js

@@ -139,6 +139,13 @@ QUnit.test("test nth_ocurrence", function(assert) {
     }
 );
 
+QUnit.test("test getSpeciesCommonName", function(assert) {
+    assert.equal(getSpeciesCommonName("homo sapiens"), "human");
+    assert.equal(getSpeciesCommonName("Homo sapiens"), "human");
+    assert.equal(getSpeciesCommonName("mus musculus"), "house mouse");
+    assert.equal(getSpeciesCommonName("gallus gallus"), "chicken");
+});
+
 QUnit.test("test tsvToArray", function(assert) {
         var tabstring = "head1\thead2\thead3\thead4\nLine 1 data1\tLine 1 data2\tLine 1 data3\tLine 1 data4\n";
         tabstring += "Line 2 data1\tLine 2 data2\tLine 2 data3\tLine 2 data4";