clone.js: hasSeg()

this.seg was always defined (to an empty object) therefore testing
whether its type is undefined was useless.
Instead we rely on a method in Clone to know whether the seg field is defined.

browser/js/axis.js

@@ -99,7 +99,7 @@ Axis.prototype = {
         //clone position
         this.pos = function(cloneID) {
             var clone = self.m.clone(cloneID) 
-            if (typeof clone.seg != "undefined" 
+            if (clone.hasSeg()
                 && typeof clone.seg[type2] != "undefined" 
                 && typeof clone.seg[type2]["name"] != 'undefined'
                 && typeof gene_list[clone.seg[type2]["name"].split("*")[0]] != "undefined")

browser/js/clone.js

@@ -142,7 +142,7 @@ Clone.prototype = {
      * Get the amino-acid sequence of the provided field (in the seg part)
      */
     getSegAASequence: function(field_name) {
-        if (typeof this.seg != 'undefined'
+        if (this.hasSeg()
             && typeof this.seg[field_name] != 'undefined'
             && typeof this.seg[field_name].aa != 'undefined') {
             return this.seg[field_name].aa;
@@ -180,7 +180,7 @@ Clone.prototype = {
      * If it does not exist return null
      */
     getSegStartStop: function(field_name) {
-        if (typeof this.seg != 'undefined'
+        if (this.hasSeg()
             && typeof this.seg[field_name] != 'undefined'
             && typeof this.seg[field_name].start != 'undefined'
             && typeof this.seg[field_name].stop != 'undefined') {
@@ -501,6 +501,10 @@ Clone.prototype = {
 
     }, //end getSize
 
+    hasSeg: function() {
+        return typeof(this.seg) != 'undefined' && ! $.isEmptyObject(this.seg)
+    },
+
     computeEValue: function () {
         var e = this.seg['evalue'];
         if (typeof(e) != 'undefined')
@@ -511,7 +515,7 @@ Clone.prototype = {
 
     getGene: function (type, withAllele) {
         withAllele = typeof withAllele !== 'undefined' ? withAllele : true;
-        if (typeof (this.seg) != 'undefined' && typeof (this.seg[type]) != 'undefined' && typeof this.seg[type]["name"] != 'undefined') {
+        if (this.hasSeg() && typeof (this.seg[type]) != 'undefined' && typeof this.seg[type]["name"] != 'undefined') {
             if (withAllele) {
                 return this.seg[type]["name"];
             }else{
@@ -530,7 +534,7 @@ Clone.prototype = {
     },
     
     getNlength: function () {
-        if (typeof this.seg != 'undefined' && typeof this.seg['3'] != 'undefined' && typeof this.seg['5'] != 'undefined'){
+        if (this.hasSeg() && typeof this.seg['3'] != 'undefined' && typeof this.seg['5'] != 'undefined'){
             return this.seg['3']['start']-this.seg['5']['stop']-1
         }else{
             return 'undefined'
@@ -566,7 +570,7 @@ Clone.prototype = {
     },
     
     getPrintableSegSequence: function () {
-        if (typeof this.seg == 'undefined' || typeof this.seg['5'] == 'undefined' || typeof this.seg['3'] == 'undefined') {
+        if (! this.hasSeg() || typeof this.seg['5'] == 'undefined' || typeof this.seg['3'] == 'undefined') {
             return this.getSequence()
         }
 
@@ -696,7 +700,7 @@ Clone.prototype = {
         }else if (this.m.colorMethod == "system") {
             this.color = this.m.germlineList.getColor(this.germline)
         } else if (this.m.colorMethod == 'productive') {
-            if (typeof this.seg != 'undefined'
+            if (this.hasSeg()
                 && typeof this.seg.junction != 'undefined'
                 && typeof this.seg.junction.productive != 'undefined') {
                 this.color = colorProductivity(this.seg.junction.productive)

browser/js/export.js

@@ -710,7 +710,7 @@ Report.prototype = {
         
         //colorized clone sequence
         var sequence = $('<div/>', {'class': 'sequence'}).appendTo(clone);
-        if (typeof this.m.clone(cloneID).seg != 'undefined'){
+        if (typeof this.m.clone(cloneID).hasSeg()){
             var seg = this.m.clone(cloneID).seg
             var seq = this.m.clone(cloneID).getSequence()
             var seqV = seq.substring(0, seg['5']['stop'] + 1)

browser/js/germline_builder.js

@@ -178,7 +178,7 @@ Germline.prototype = {
         //and add undetected genes (missing from germline)
         var g = {}
         for (var i=0; i<this.m.clones.length; i++){
-            if (typeof this.m.clone(i).seg != "undefined" &&
+            if (typeof this.m.clone(i).hasSeg() != "undefined" &&
                 typeof this.m.clone(i).seg[type2] != "undefined" &&
                 typeof this.m.clone(i).seg[type2]["name"] != "undefined"
             ){

browser/js/model_loader.js

@@ -712,7 +712,7 @@ Model_loader.prototype = {
         var count = 0;
         
         for (var i in this.clones){
-            if (typeof this.clones[i].seg != "undefined" && typeof this.clones[i].seg.quality != "undefined"){
+            if (typeof this.clones[i].hasSeg() && typeof this.clones[i].seg.quality != "undefined"){
                 var s = this.clones[i].seg.quality.seq;
                 for (var j in s){
                     if (s[j] != "!"){

browser/js/segmenter.js

@@ -874,7 +874,7 @@ Segment.prototype = {
             }
             
             // In the .seg element, What looks like DNA sequence or what is a Pos field
-            if (typeof clone.seg != 'undefined'){
+            if (clone.hasSeg()){
                 for (var i in clone.seg) {
                     if (! forbidden_fields.includes(i) &&(this.isDNA(clone.seg[i]) || this.isPos(clone.seg[i])) ){
                         if (result.indexOf(i) == -1) result.push(i);
@@ -1044,7 +1044,7 @@ Sequence.prototype = {
         var stop = -1;
                 
         var clone = this.m.clone(this.id);
-        if (typeof clone.seg != "undefined" && typeof clone.seg["cdr3"] != "undefined"){
+        if (clone.hasSeg() && typeof clone.seg["cdr3"] != "undefined"){
             if (typeof clone.seg["cdr3"].start != "undefined") {
                 start = this.pos[clone.seg["cdr3"].start];
                 stop = this.pos[clone.seg["cdr3"].stop];
@@ -1112,7 +1112,7 @@ Sequence.prototype = {
         if (typeof clone.sequence != 'undefined' && clone.sequence != 0) {
 
             //find V, D, J position
-            if (typeof clone.seg != 'undefined'){
+            if (clone.hasSeg()){
 
                 var vdjArray = this.getVdjStartEnd(clone);
                 var vdjArrayRev = {};
@@ -1139,7 +1139,7 @@ Sequence.prototype = {
             }
 
             var window_start = this.pos[clone.sequence.indexOf(clone.id)];
-            if (typeof clone.seg != "undefined" && typeof clone.seg["cdr3"] != "undefined"){
+            if (clone.hasSeg() && typeof clone.seg["cdr3"] != "undefined"){
                 if (clone.seg["cdr3"].start != "undefined"){
                     window_start = this.pos[clone.seg["cdr3"].start];
                 }else if (clone.seg["cdr3"].constructor === String){
@@ -1260,7 +1260,7 @@ Sequence.prototype = {
         // Find the good object p
         if (typeof clone[field] != 'undefined'){
             p = clone[field];                   //check clone meta-data
-        }else if (typeof clone.seg != 'undefined' && typeof clone.seg[field] != 'undefined'){
+        }else if (clone.hasSeg() && typeof clone.seg[field] != 'undefined'){
             p = clone.seg[field];               //check clone seg data
         }else if (typeof this.m[field] != 'undefined'){
             p = this.m[field];               //check model