browser : replace windows with clones object

browser/js/axis.js

@@ -139,7 +139,7 @@ Axis.prototype = {
         
         var n_min = 0;
         var n_max = 1;
-        for (var i=0; i<this.m.n_windows; i++){
+        for (var i=0; i<this.m.n_clones; i++){
             if (this.m.clone(i).Nlength > n_max) n_max = this.m.clone(i).Nlength;
         }
         

browser/js/builder.js

@@ -112,7 +112,7 @@ Builder.prototype = {
         normalize_list.appendChild(document.createTextNode("none"))
         normalize_list.appendChild(document.createElement("br"))
         
-        for (var i=0; i<self.m.n_windows; i++){
+        for (var i=0; i<self.m.n_clones; i++){
             if (typeof self.m.clone(i).expected != "undefined"){
                 var input = document.createElement("input")
                 var text = document.createTextNode(self.m.clone(i).getName() + " => " +self.m.clone(i).expected)
@@ -357,7 +357,7 @@ Builder.prototype = {
 
         //init slider
         var max_top = 0;
-        for (var i = 0; i < this.m.n_windows; i++) {
+        for (var i = 0; i < this.m.n_clones; i++) {
             if (this.m.clone(i).top > max_top)
                 max_top = this.m.clone(i).top
         }
@@ -410,7 +410,7 @@ Builder.prototype = {
         var clusterSelector = document.getElementById("clusterby_button")
         clusterSelector.innerHTML = "";
         
-        if (self.m.windows[0]._target){
+        if (self.m.clones[0]._target){
         
             var target = document.createElement('a');
                 target.className = "buttonSelector"
@@ -437,7 +437,7 @@ Builder.prototype = {
             clusterSelector.appendChild(clonotype)
         }
         
-        if (self.m.windows[0].system){
+        if (self.m.clones[0].system){
             
             var system = document.createElement('a');
                 system.className = "buttonSelector"

browser/js/clone.js

@@ -64,7 +64,7 @@ Clone.prototype = {
         }
     }, 
 
-    /* compute the clone size ( sum of all windows clustered )
+    /* compute the clone size ( sum of all clones clustered )
      * @t : tracking point (default value : current tracking point)
      * */
     getSize: function (time) {
@@ -107,7 +107,7 @@ Clone.prototype = {
     }, //end getSequenceSize
 
 
-    /* compute the clone reads number ( sum of all reads of windows clustered )
+    /* compute the clone reads number ( sum of all reads of clones clustered )
      * @t : tracking point (default value : current tracking point)
      * */
     getReads: function (time) {

browser/js/germline_builder.js

@@ -50,7 +50,7 @@ Germline.prototype = {
         //reduce germline size (keep only detected genes)
         //and add undetected genes 
         var g = {}
-        for (var i=0; i<this.m.n_windows; i++){
+        for (var i=0; i<this.m.n_clones; i++){
             if (typeof this.m.clone(i)[type] != "undefined" 
                 && typeof this.m.clone(i)[type][0] != "undefined"){
                 var gene=this.m.clone(i)[type][0];

browser/js/graph.js

@@ -136,7 +136,7 @@ Graph.prototype = {
 
         this.initAxis();
 
-        for (var i = 0; i < this.m.n_windows; i++) {
+        for (var i = 0; i < this.m.n_clones; i++) {
             this.data_graph[i] = {
                 id: i,
                 name: "line" + i,
@@ -153,13 +153,13 @@ Graph.prototype = {
         }
 
         this.data_res.push({
-            id: this.m.n_windows,
+            id: this.m.n_clones,
             name: "resolution1",
             path: this.constructPathR(this.resolution1)
         });
         
         this.data_res.push({
-            id: this.m.n_windows + 1,
+            id: this.m.n_clones + 1,
             name: "resolution5",
             path: this.constructPathR(this.resolution5)
         });
@@ -398,12 +398,12 @@ Graph.prototype = {
             this.data_res[0].path = this.constructPathR(this.resolution1);
             this.data_res[1].path = this.constructPathR(this.resolution5);
 
-            for (var i = 0; i < this.m.n_windows; i++) {
+            for (var i = 0; i < this.m.n_clones; i++) {
                 for (var j = 0; j < this.m.clusters[i].length; j++) {
                     this.data_graph[this.m.clusters[i][j]].path = this.constructPath(i, false);
                 }
             }
-            for (var i = 0; i < this.m.n_windows; i++) {
+            for (var i = 0; i < this.m.n_clones; i++) {
                 var cloneID = i
                 for (var j = 0; j < this.m.clusters[cloneID].length; j++) {
                     var seqID = this.m.clusters[cloneID][j]
@@ -892,11 +892,11 @@ Stack.prototype = {
         this.total_size = []; 
         for (j=0; j<this.m.samples.number; j++){
             this.total_size[j]=0
-            for (i=0; i<this.m.n_windows; i++){
+            for (i=0; i<this.m.n_clones; i++){
                 if (this.m.clone(i).isActive()) this.total_size[j] += this.m.clone(i).getSize(j); //active clones
             }
             
-            this.total_size[j] += this.m.clone(this.m.windows.length-1).getSize(j);//other clones
+            this.total_size[j] += this.m.clone(this.m.clones.length-1).getSize(j);//other clones
         }
     },
     
@@ -909,7 +909,7 @@ Stack.prototype = {
             this.sum[j]=1
         }
         
-        for (i=0; i<this.m.n_windows; i++){
+        for (i=0; i<this.m.n_clones; i++){
             this.min[i] = []
             this.max[i] = []
             //active clones
@@ -929,9 +929,9 @@ Stack.prototype = {
         
         //other
         for (j=0; j<this.m.samples.number; j++){
-            this.min[this.m.windows.length-1][j] = this.sum[j]
-            this.sum[this.m.windows.length-1] += this.m.clone(this.m.windows.length-1).getSize(j)
-            this.max[this.m.windows.length-1][j] = this.sum[j]
+            this.min[this.m.clones.length-1][j] = this.sum[j]
+            this.sum[this.m.clones.length-1] += this.m.clone(this.m.clones.length-1).getSize(j)
+            this.max[this.m.clones.length-1][j] = this.sum[j]
         }
         
     },

browser/js/list.js

@@ -60,7 +60,7 @@ List.prototype = {
         var div_list_clones = document.createElement('div')
         div_list_clones.id = "list_clones"
 
-        for (var i = 0; i < this.m.n_windows; i++) {
+        for (var i = 0; i < this.m.n_clones; i++) {
             var div = document.createElement('li');
             div.className = "list";
             div.id = i;
@@ -158,7 +158,7 @@ List.prototype = {
         var startTime = new Date()
             .getTime();
         var elapsedTime = 0;
-        for (var i = 0; i < this.m.n_windows; i++) {
+        for (var i = 0; i < this.m.n_clones; i++) {
             this.updateElem([i]);
         }
         elapsedTime = new Date()
@@ -472,7 +472,7 @@ List.prototype = {
     },
     
     reset_filter: function (bool) {
-        for (var i=0; i<this.m.n_windows; i++){
+        for (var i=0; i<this.m.n_clones; i++){
             var c = this.m.clone(i)
             c.isFiltered=bool
         }
@@ -480,7 +480,7 @@ List.prototype = {
     
     filter: function (str) {
         this.reset_filter(true)
-        for (var i=0; i<this.m.n_windows; i++){
+        for (var i=0; i<this.m.n_clones; i++){
             var c = this.m.clone(i) 
             if (c.getName().toUpperCase().indexOf(str.toUpperCase())!=-1 ) c.isFiltered = false
             if (c.getSequence().toUpperCase().indexOf(str.toUpperCase())!=-1 ) c.isFiltered = false

browser/js/pdf.js

@@ -41,7 +41,7 @@ PDF.prototype = {
 
         if (this.list.length == 0) {
             var flag = 5;
-            for (var i = 0; i < this.m.n_windows; i++) {
+            for (var i = 0; i < this.m.n_clones; i++) {
                 if (this.m.clusters[i].length != 0 && flag != 0) {
                     this.list.push(i);
                     flag--;
@@ -182,7 +182,7 @@ PDF.prototype = {
         opt2.y_offset = opt.y;
 
         //clones style
-        for (var i = 0; i < this.m.n_windows; i++) {
+        for (var i = 0; i < this.m.n_clones; i++) {
             var polyline = elem.querySelectorAll('[id="polyline'+i+'"]')[0]
             var color = tagColor[this.m.clone(i).getTag()]
 
@@ -194,7 +194,7 @@ PDF.prototype = {
                 polyline.setAttribute("stroke", color);
             }
 
-            if (m.windows[i].window == "other" || !m.windows[i].active) {
+            if (m.clone(i).window == "other" || !m.clone(i).isActive()) {
                 polyline.parentNode.removeChild(polyline);
             }
         }
@@ -378,9 +378,9 @@ PDF.prototype = {
         this.doc.setFont('courier', 'normal');
         this.doc.setTextColor(0, 0, 0)
 
-        if (typeof (m.windows[cloneID].sequence) != 'number') {
+        if (m.clone(cloneID).getSequence() != "0") {
 
-            var seq = m.windows[cloneID].sequence;
+            var seq = m.clone(cloneID).getSequence()
             var seqV = seq.substring(0, this.m.clone(cloneID).Vend + 1)
             var seqN = seq.substring(this.m.clone(cloneID).Vend + 1, this.m.clone(cloneID).Jstart)
             var seqJ = seq.substring(this.m.clone(cloneID).Jstart)
@@ -426,7 +426,7 @@ PDF.prototype = {
             }
 
         } else {
-            this.doc.text(this.marge + 20, this.y, "segment fail :" + m.windows[cloneID].window);
+            this.doc.text(this.marge + 20, this.y, "segment fail :" + m.clone(cloneID).window);
         }
 
         this.y += 5;
@@ -462,7 +462,7 @@ PDF.prototype = {
     
     icon: function (cloneID, x, y, w, h) {
 
-        var color = tagColor[m.windows[cloneID].tag]
+        var color = tagColor[m.clone(cloneID).tag]
 
         var polyline = document.getElementById("polyline" + cloneID)
             .cloneNode(true);

browser/js/scatterPlot.js

@@ -215,9 +215,9 @@ ScatterPlot.prototype = {
       this.grpLinks = this.plot_container.append('svg:g').attr('class', 'grpLinks');
 
       //Initialisation des nodes
-      this.nodes = d3.range(this.m.n_windows)
+      this.nodes = d3.range(this.m.n_clones)
 	  .map(Object);
-      for (var i = 0; i < this.m.n_windows; i++) {
+      for (var i = 0; i < this.m.n_clones; i++) {
 	  this.nodes[i].id = i; //L'id d'un cercle vaut le nombre de i dans la boucle
 	  this.nodes[i].r1 = 5; // longueur du rayon1
 	  this.nodes[i].r2 = 5; // longueur du rayon2
@@ -280,14 +280,14 @@ ScatterPlot.prototype = {
 
   },
 
-  /* Function which allows to return the number of active windows
+  /* Function which allows to return the number of active clones
   */
-  returnActiveWindows: function() {
-    var activeWindows = 0;
-    for (var i=0; i<this.m.n_windows;i++) {
-      if (this.m.clone(i).isActive()) activeWindows += 1;
+  returnActiveclones: function() {
+    var activeclones = 0;
+    for (var i=0; i<this.m.n_clones;i++) {
+      if (this.m.clone(i).isActive()) activeclones += 1;
     }
-    return activeWindows;
+    return activeclones;
   },
 
   /* Function which allows to initialize the D3JS engine - usefull with reinitMotor()
@@ -682,7 +682,7 @@ ScatterPlot.prototype = {
       }
 
       //classement des clones suivant V
-      for (var i = 0; i < this.m.n_windows; i++) {
+      for (var i = 0; i < this.m.n_clones; i++) {
 	  if (this.m.clone(i).isActive()) {
 	      var geneV = this.m.clone(i).getV();
 	      var clone = {
@@ -1135,7 +1135,7 @@ ScatterPlot.prototype = {
   /* Function which permits to force all no-clustered clones, to return at their initial position
   */
   forceNodesToStayInInitialPosition: function() {
-      for (var i = 0; i < this.m.n_windows; i++) {
+      for (var i = 0; i < this.m.n_clones; i++) {
           if (this.m.dbscan.clusters[this.m.clone(i).cluster].length == 1) {
               //Calcul du delta
               var x = this.nodes[i].x;

browser/js/segmenter.js

@@ -187,7 +187,7 @@ Segment.prototype = {
      *
      * */
     update: function () {
-        for (var i = 0; i < this.m.n_windows; i++) {
+        for (var i = 0; i < this.m.n_clones; i++) {
             this.updateElem([i]);
         }
     },