model.js: store tag info to model.js

remove tag from global var

browser/js/builder.js

@@ -188,7 +188,7 @@ Builder.prototype = {
         //reset
         listTag.innerHTML = "";
 
-        for (var i = 0; i < tag.length; i++) {
+        for (var i = 0; i < this.m.tag.length; i++) {
             (function (i) {
                 var span3 = document.createElement('span');
                 span3.onclick = function (tag) {
@@ -310,7 +310,7 @@ Builder.prototype = {
         var input = document.createElement('input');
         input.type = "text";
         input.id = "new_tag_name";
-        input.value = tag[tagID].name;
+        input.value = this.m.tag[tagID].name;
         input.style.width = "100px";
         input.style.border = "0px";
         input.style.margin = "0px";
@@ -339,7 +339,7 @@ Builder.prototype = {
             event.preventDefault()
             var newTagName = document.getElementById("new_tag_name")
                 .value;
-            tag[tagID].name = newTagName
+            this.m.tag[tagID].name = newTagName
             self.build_tagSelector()
             self.build_displaySelector()
             self.m.analysisHasChanged = true
@@ -407,7 +407,7 @@ Builder.prototype = {
         listGermline.innerHTML = "";
 
         //init tag list
-        for (var i = 0; i < tag.length; i++) {
+        for (var i = 0; i < this.m.tag.length; i++) {
             (function (i) {
                 var span3 = document.createElement('span');
                 span3.onclick = function (tag) {
@@ -834,7 +834,7 @@ Builder.prototype = {
             break;
         case "Tag":
 
-            for (var i = 0; i < tag.length; i++) {
+            for (var i = 0; i < this.m.tag.length; i++) {
                 var spantag = document.createElement('span');
                 spantag.className = "tagColorBox tagColor" + i
                 spantag.id = "fastTag" + i
@@ -865,17 +865,17 @@ Builder.prototype = {
     },
     
     initTag: function (){
-        for (var i =0; i<tag.length; i++){
-            $(".tagColor"+i).prop("title", tag[i].name);
-            $(".tagName"+i).html(tag[i].name);
+        for (var i =0; i<this.m.tag.length; i++){
+            $(".tagColor"+i).prop("title", this.m.tag[i].name);
+            $(".tagName"+i).html(this.m.tag[i].name);
         }
         this.updateTagBox();
     },
     
   
     updateTagBox: function(){
-        for (var i =0; i<tag.length; i++){
-            if (tag[i].display){
+        for (var i =0; i<this.m.tag.length; i++){
+            if (this.m.tag[i].display){
                 $(".tagColor"+i).removeClass("inactiveTag")
             }else{
                 $(".tagColor"+i).addClass("inactiveTag")
@@ -885,8 +885,8 @@ Builder.prototype = {
     
     nextDisplayTag: function(elem){
         var id_tag = elem.id.charAt( elem.id.length-1 ) 
-        var s = tag[id_tag].display;
-        tag[id_tag].display = !s;
+        var s = this.m.tag[id_tag].display;
+        this.m.tag[id_tag].display = !s;
         this.m.update();
     },
     

browser/js/clone.js

@@ -372,12 +372,12 @@ Clone.prototype = {
         if (this.tag) {
             return this.tag;
         } else {
-            return default_tag;
+            return this.m.default_tag;
         }
     }, 
     
     getTagName: function () {
-        return tag[this.getTag()].name
+        return this.m.tag[this.getTag()].name
     }, 
     
     
@@ -393,10 +393,10 @@ Clone.prototype = {
             if (size == 0){
                 this.color = "";
             }else{
-                this.color = colorGenerator(this.m.scale_color(size * this.m.precision), color_s, color_v);
+                this.color = colorGenerator(this.m.scale_color(size * this.m.precision));
             }
         }else if (this.m.colorMethod == "Tag"){
-            this.color =  tag[this.getTag()].color;
+            this.color =  this.m.tag[this.getTag()].color;
         }else if (this.m.colorMethod == "dbscan"){
             this.color =  this.colorDBSCAN;
         }else if (this.m.colorMethod == "V" && this.getV() != "undefined V"){
@@ -536,7 +536,7 @@ Clone.prototype = {
     },
     
     enable: function (top) {
-        if (this.top <= top && tag[this.getTag()].display && this.id != "other") {
+        if (this.top <= top && this.m.tag[this.getTag()].display && this.id != "other") {
             this.active = true;
         }
     },

browser/js/germline_builder.js

@@ -185,15 +185,13 @@ Germline.prototype = {
                 var tmp = this.allele[key[i]];
                 this.allele[key[i]] = {};
                 this.allele[key[i]].seq = tmp;
-                this.allele[key[i]].color = colorGenerator((30 + (i / key.length) * 290),
-                    color_s, color_v);
+                this.allele[key[i]].color = colorGenerator((30 + (i / key.length) * 290));
 
                 var elem = key[i].split('*')[0];
                 if (elem != elem2) {
                     this.gene[elem2] = {};
                     this.gene[elem2].n = n2;
-                    this.gene[elem2].color = colorGenerator((30 + ((i - 1) / key.length) * 290),
-                        color_s, color_v);
+                    this.gene[elem2].color = colorGenerator((30 + ((i - 1) / key.length) * 290));
                     this.gene[elem2].rank = n;
                     n++;
                     n2 = 0;
@@ -206,8 +204,7 @@ Germline.prototype = {
             this.gene[elem2] = {};
             this.gene[elem2].n = n2;
             this.gene[elem2].rank = n
-            this.gene[elem2].color = colorGenerator((30 + ((i - 1) / key.length) * 290),
-                color_s, color_v);
+            this.gene[elem2].color = colorGenerator((30 + ((i - 1) / key.length) * 290));
         }
         
         return callback

browser/js/list.js

@@ -322,7 +322,7 @@ List.prototype = {
         var path = document.createElementNS('http://www.w3.org/2000/svg', 'path')
         path.setAttribute('d', this.starPath);
         path.setAttribute('id', 'color' + cloneID);
-        path.setAttribute("fill", tag[this.m.clone(cloneID).getTag()].color);
+        path.setAttribute("fill", this.m.tag[this.m.clone(cloneID).getTag()].color);
         svg.appendChild(path);
         span_star.appendChild(svg)
 

browser/js/main.js

@@ -16,7 +16,7 @@ var segment = new Segment("bot-container",m);
 
 var builder = new Builder(m);
 var pdf = new PDF(m, "visu2_svg")
-var report = new Report()
+var report = new Report(m)
 var db = new Database("plop!", m);
 
 

browser/js/menu.js

@@ -64,6 +64,12 @@ function initMenu () {
     }
 }
 
+function changeStyle(newStyle){
+    if (newStyle=="solarizeD") document.getElementById("palette").href="css/dark.css";
+    if (newStyle=="solarizeL") document.getElementById("palette").href="css/light.css";
+    m.update()
+}
+
 function loadData() {
     
     myConsole.closePopupMsg()

browser/js/model.js

@@ -98,7 +98,6 @@ Model.prototype = {
         this.nbr = 0;
         this.nodes = null;
         this.edges = null;
-
         this.cluster_key = ""
         
         //segmented status
@@ -117,9 +116,25 @@ Model.prototype = {
             "= SEG, but no window",
         ];
 
+        this.tag = [
+            {"color" : "#dc322f", "name" : "clone 1", "display" : true},
+            {"color" : "#cb4b16", "name" : "clone 2", "display" : true},
+            {"color" : "#b58900", "name" : "clone 3", "display" : true},
+            {"color" : "#268bd2", "name" : "standard", "display" : true},
+            {"color" : "#6c71c4", "name" : "standard (noise)", "display" : true},
+            {"color" : "#2aa198", "name" : "custom 1", "display" : true},
+            {"color" : "#d33682", "name" : "custom 2", "display" : true},
+            {"color" : "#859900", "name" : "custom 3", "display" : true},
+            {"color" : "", "name" : "-/-", "display" : true}
+        ]
+
+        this.default_tag=8;
+        
     },
     
     
+    
+    
     start: function() {
         var self = this;
         var dataURL = ""
@@ -475,11 +490,11 @@ Model.prototype = {
                 
                 var keys = Object.keys(s.names);
                 for (var i=0; i<keys.length; i++){
-                    tag[parseInt(keys[i])].name = s.names[keys[i]]
+                    this.tag[parseInt(keys[i])].name = s.names[keys[i]]
                 }
                 
                 for (var i=0; i<s.hide.length; i++){
-                    tag[s.hide[i]].display = false;
+                    this.tag[s.hide[i]].display = false;
                 }
             }
             
@@ -544,7 +559,7 @@ Model.prototype = {
         //      COLOR_N
         for (var i = 0; i < this.clones.length; i++) {
             var clone = this.clone(i)
-            clone.colorN = colorGenerator((((clone.getNlength() / n_max) - 1) * (-250)), color_s, color_v);
+            clone.colorN = colorGenerator((((clone.getNlength() / n_max) - 1) * (-250)));
         }
         
         this.applyAnalysis(this.analysis);
@@ -559,7 +574,7 @@ Model.prototype = {
         for (key in this.data){
             if (this.data[key].length == this.samples.number){
                 this.data_info[key] = {
-                    "color" : tag[i].color,
+                    "color" : this.tag[i].color,
                     "isActive" : false
                 }
                 i++
@@ -741,9 +756,9 @@ Model.prototype = {
         //tags
         analysisData.tags.names = {}
         analysisData.tags.hide = []
-        for (var i=0; i<tag.length; i++){
-            analysisData.tags.names[""+i] = tag[i].name
-            if (!tag[i].display) analysisData.tags.hide.push(i)
+        for (var i=0; i<this.tag.length; i++){
+            analysisData.tags.names[""+i] = this.tag[i].name
+            if (!this.tag[i].display) analysisData.tags.hide.push(i)
         }
         
         
@@ -2027,7 +2042,7 @@ Model.prototype = {
         var maxCluster = this.dbscan.clusters.length;
         for (var i = 0; i < this.clones.length; i++) {
             if (typeof(this.clone(i)) != 'undefined') {
-                this.clone(i).colorDBSCAN = colorGenerator( ( (270 / maxCluster) * (this.tabRandomColor[this.clone(i)] + 1) ), color_s, color_v);
+                this.clone(i).colorDBSCAN = colorGenerator( ( (270 / maxCluster) * (this.tabRandomColor[this.clone(i)] + 1) ));
             }
             else
                 this.clone(i).colorDBSCAN = "";

browser/js/pdf.js

@@ -190,7 +190,7 @@ PDF.prototype = {
         //clones style
         for (var i = 0; i < this.m.clones.length; i++) {
             var polyline = elem.querySelectorAll('[id="polyline'+i+'"]')[0]
-            var color = tag[this.m.clone(i).getTag()].color
+            var color = this.m.tag[this.m.clone(i).getTag()].color
 
             if (polyline.getAttribute("d").indexOf("Z") != -1){
                 polyline.setAttribute("style", "stroke-width:0px");
@@ -208,7 +208,7 @@ PDF.prototype = {
         //selected clones style
         for (var i = 0; i < this.list.length; i++) {
             var polyline = elem.querySelectorAll('[id="polyline'+this.list[i]+'"]')[0] 
-            var color = tag[this.m.clone(this.list[i]).getTag()].color
+            var color = this.m.tag[this.m.clone(this.list[i]).getTag()].color
 
             polyline.setAttribute("stroke", color);
             polyline.setAttribute("style", "stroke-width: "+opt.strokeSize+"px");
@@ -345,7 +345,7 @@ PDF.prototype = {
     info_clone: function (cloneID) {
         this.checkPage(20)
 
-        var color = tag[this.m.clone(cloneID).getTag()].color
+        var color = this.m.tag[this.m.clone(cloneID).getTag()].color
 
         this.icon(cloneID, this.marge, this.y - 6, 18, 8)
 
@@ -472,7 +472,7 @@ PDF.prototype = {
     
     icon: function (cloneID, x, y, w, h) {
 
-        var color = tag[m.clone(cloneID).tag].color
+        var color = this.m.tag[m.clone(cloneID).tag].color
 
         var polyline = document.getElementById("polyline" + cloneID)
             .cloneNode(true);

browser/js/scatterPlot.js

@@ -521,7 +521,7 @@ ScatterPlot.prototype = {
                 //If the link's length is lower than distanceMax, color the link
                 if (this.edge[i].len <= this.distanceMax)
                 //colorGenerator usage for color red (0) to blue (270), by gap: 270/distanceMax
-                    this.edge[i].color = colorGenerator((270 / this.distanceMax) * this.edge[i].len, color_s, color_v);
+                    this.edge[i].color = colorGenerator((270 / this.distanceMax) * this.edge[i].len);
                 //If the link is not interesting, we attribute the white color (usefull for the activeAllLine() function)
                 else this.edge[i].color = "white";
             }

browser/js/segmenter.js

@@ -421,7 +421,7 @@ Segment.prototype = {
         var path = document.createElementNS('http://www.w3.org/2000/svg', 'path')
         path.setAttribute('d', this.starPath);
         path.setAttribute('id', 'color' + cloneID);
-        if (typeof this.m.clone(cloneID).tag != 'undefined') path.setAttribute("fill", tag[this.m.clone(cloneID).tag].color);
+        if (typeof this.m.clone(cloneID).tag != 'undefined') path.setAttribute("fill", this.m.tag[this.m.clone(cloneID).tag].color);
         else path.setAttribute("fill", "");
 
         svg_star.appendChild(path);

browser/js/vidjil-style.js

@@ -21,26 +21,11 @@
  * along with "Vidjil". If not, see <http://www.gnu.org/licenses/>
  */
 
-var color_s = 0.8; //pureté
-var color_v = 0.72; //brightness
-
-
-tag = [
-        {"color" : "#dc322f", "name" : "clone 1", "display" : true},
-        {"color" : "#cb4b16", "name" : "clone 2", "display" : true},
-        {"color" : "#b58900", "name" : "clone 3", "display" : true},
-        {"color" : "#268bd2", "name" : "standard", "display" : true},
-        {"color" : "#6c71c4", "name" : "standard (noise)", "display" : true},
-        {"color" : "#2aa198", "name" : "custom 1", "display" : true},
-        {"color" : "#d33682", "name" : "custom 2", "display" : true},
-        {"color" : "#859900", "name" : "custom 3", "display" : true},
-        {"color" : "", "name" : "-/-", "display" : true}
-    ]
-
-var default_tag=8;
   
   /*ressort une couleur format RGB*/
   function colorGenerator(h,s,v){
+    s = typeof s !== 'undefined' ? s : 0.8
+    v = typeof v !== 'undefined' ? v : 0.72
     h=h/60;
     var i=Math.floor(h);
     var f=h-i;
@@ -69,11 +54,5 @@ var default_tag=8;
     }
   }
 
-      
-  function changeStyle(newStyle){
-	if (newStyle=="solarizeD") document.getElementById("palette").href="css/dark.css";
-	if (newStyle=="solarizeL") document.getElementById("palette").href="css/light.css";
-    m.update()
-  }