gene variants can store information about amino acid change

frontend-js/src/main/js/map/data/GeneVariant.js

@@ -9,7 +9,8 @@
  * @param {string} javaObject.referenceGenomeType
  * @param {string} javaObject.referenceGenomeVersion
  * @param {string} javaObject.contig
- * @param {null|number} [javaObject.allelFrequency]
+ * @param {string} [javaObject.aminoAcidChange]
+ * @param {null|string} [javaObject.allelFrequency]
  * @param {null|string} [javaObject.variantIdentifier]
  *
  * @constructor
@@ -23,8 +24,25 @@ function GeneVariant(javaObject) {
   this.setContig(javaObject.contig);
   this.setAllelFrequency(javaObject.allelFrequency);
   this.setVariantIdentifier(javaObject.variantIdentifier);
+  this.setAminoAcidChange(javaObject.aminoAcidChange);
 }
 
+/**
+ *
+ * @param {string} aminoAcidChange
+ */
+GeneVariant.prototype.setAminoAcidChange = function (aminoAcidChange) {
+  this._aminoAcidChange = aminoAcidChange;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getAminoAcidChange = function () {
+  return this._aminoAcidChange;
+};
+
 /**
  *
  * @param {number} position
@@ -91,13 +109,13 @@ GeneVariant.prototype.getContig = function () {
 
 /**
  *
- * @param {number} allelFrequency
+ * @param {string} allelFrequency
  */
 GeneVariant.prototype.setAllelFrequency = function (allelFrequency) {
   if (allelFrequency === null) {
     this._allelFrequency = undefined;
   } else {
-    this._allelFrequency = allelFrequency;
+    this._allelFrequency = parseFloat(allelFrequency);
   }
 };
 

frontend-js/src/test/js/map/data/GeneVariant-test.js

@@ -5,6 +5,7 @@ var assert = require('assert');
 
 describe('GeneVariant', function () {
   it("constructor", function () {
+    // noinspection SpellCheckingInspection
     var data = {
       position: 12,
       originalDna: "A",
@@ -13,7 +14,8 @@ describe('GeneVariant', function () {
       referenceGenomeVersion: "v1",
       contig: "1",
       allelFrequency: "0.2",
-      variantIdentifier: "id"
+      variantIdentifier: "id",
+      aminoAcidChange: "LRRK2:NM_198578:exon1:c.T45C:p.T15T"
     };
     var variant = new GeneVariant(data);
     assert.equal(variant.getPosition(), data.position);
@@ -24,5 +26,6 @@ describe('GeneVariant', function () {
     assert.equal(variant.getAllelFrequency(), data.allelFrequency);
     assert.equal(variant.getVariantIdentifier(), data.variantIdentifier);
     assert.equal(variant.getReferenceGenomeVersion(), data.referenceGenomeVersion);
+    assert.equal(variant.getAminoAcidChange(), data.aminoAcidChange);
   });
 });