Commit 8057f332 authored by Marc Duez's avatar Marc Duez

browser : replace windows with clones object

parent 8d9c9b2b
...@@ -139,7 +139,7 @@ Axis.prototype = { ...@@ -139,7 +139,7 @@ Axis.prototype = {
var n_min = 0; var n_min = 0;
var n_max = 1; 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; if (this.m.clone(i).Nlength > n_max) n_max = this.m.clone(i).Nlength;
} }
......
...@@ -112,7 +112,7 @@ Builder.prototype = { ...@@ -112,7 +112,7 @@ Builder.prototype = {
normalize_list.appendChild(document.createTextNode("none")) normalize_list.appendChild(document.createTextNode("none"))
normalize_list.appendChild(document.createElement("br")) 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"){ if (typeof self.m.clone(i).expected != "undefined"){
var input = document.createElement("input") var input = document.createElement("input")
var text = document.createTextNode(self.m.clone(i).getName() + " => " +self.m.clone(i).expected) var text = document.createTextNode(self.m.clone(i).getName() + " => " +self.m.clone(i).expected)
...@@ -357,7 +357,7 @@ Builder.prototype = { ...@@ -357,7 +357,7 @@ Builder.prototype = {
//init slider //init slider
var max_top = 0; 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) if (this.m.clone(i).top > max_top)
max_top = this.m.clone(i).top max_top = this.m.clone(i).top
} }
...@@ -410,7 +410,7 @@ Builder.prototype = { ...@@ -410,7 +410,7 @@ Builder.prototype = {
var clusterSelector = document.getElementById("clusterby_button") var clusterSelector = document.getElementById("clusterby_button")
clusterSelector.innerHTML = ""; clusterSelector.innerHTML = "";
if (self.m.windows[0]._target){ if (self.m.clones[0]._target){
var target = document.createElement('a'); var target = document.createElement('a');
target.className = "buttonSelector" target.className = "buttonSelector"
...@@ -437,7 +437,7 @@ Builder.prototype = { ...@@ -437,7 +437,7 @@ Builder.prototype = {
clusterSelector.appendChild(clonotype) clusterSelector.appendChild(clonotype)
} }
if (self.m.windows[0].system){ if (self.m.clones[0].system){
var system = document.createElement('a'); var system = document.createElement('a');
system.className = "buttonSelector" system.className = "buttonSelector"
......
...@@ -64,7 +64,7 @@ Clone.prototype = { ...@@ -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) * @t : tracking point (default value : current tracking point)
* */ * */
getSize: function (time) { getSize: function (time) {
...@@ -107,7 +107,7 @@ Clone.prototype = { ...@@ -107,7 +107,7 @@ Clone.prototype = {
}, //end getSequenceSize }, //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) * @t : tracking point (default value : current tracking point)
* */ * */
getReads: function (time) { getReads: function (time) {
......
...@@ -50,7 +50,7 @@ Germline.prototype = { ...@@ -50,7 +50,7 @@ Germline.prototype = {
//reduce germline size (keep only detected genes) //reduce germline size (keep only detected genes)
//and add undetected genes //and add undetected genes
var g = {} 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" if (typeof this.m.clone(i)[type] != "undefined"
&& typeof this.m.clone(i)[type][0] != "undefined"){ && typeof this.m.clone(i)[type][0] != "undefined"){
var gene=this.m.clone(i)[type][0]; var gene=this.m.clone(i)[type][0];
......
...@@ -136,7 +136,7 @@ Graph.prototype = { ...@@ -136,7 +136,7 @@ Graph.prototype = {
this.initAxis(); 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] = { this.data_graph[i] = {
id: i, id: i,
name: "line" + i, name: "line" + i,
...@@ -153,13 +153,13 @@ Graph.prototype = { ...@@ -153,13 +153,13 @@ Graph.prototype = {
} }
this.data_res.push({ this.data_res.push({
id: this.m.n_windows, id: this.m.n_clones,
name: "resolution1", name: "resolution1",
path: this.constructPathR(this.resolution1) path: this.constructPathR(this.resolution1)
}); });
this.data_res.push({ this.data_res.push({
id: this.m.n_windows + 1, id: this.m.n_clones + 1,
name: "resolution5", name: "resolution5",
path: this.constructPathR(this.resolution5) path: this.constructPathR(this.resolution5)
}); });
...@@ -398,12 +398,12 @@ Graph.prototype = { ...@@ -398,12 +398,12 @@ Graph.prototype = {
this.data_res[0].path = this.constructPathR(this.resolution1); this.data_res[0].path = this.constructPathR(this.resolution1);
this.data_res[1].path = this.constructPathR(this.resolution5); 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++) { for (var j = 0; j < this.m.clusters[i].length; j++) {
this.data_graph[this.m.clusters[i][j]].path = this.constructPath(i, false); 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 var cloneID = i
for (var j = 0; j < this.m.clusters[cloneID].length; j++) { for (var j = 0; j < this.m.clusters[cloneID].length; j++) {
var seqID = this.m.clusters[cloneID][j] var seqID = this.m.clusters[cloneID][j]
...@@ -892,11 +892,11 @@ Stack.prototype = { ...@@ -892,11 +892,11 @@ Stack.prototype = {
this.total_size = []; this.total_size = [];
for (j=0; j<this.m.samples.number; j++){ for (j=0; j<this.m.samples.number; j++){
this.total_size[j]=0 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 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 = { ...@@ -909,7 +909,7 @@ Stack.prototype = {
this.sum[j]=1 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.min[i] = []
this.max[i] = [] this.max[i] = []
//active clones //active clones
...@@ -929,9 +929,9 @@ Stack.prototype = { ...@@ -929,9 +929,9 @@ Stack.prototype = {
//other //other
for (j=0; j<this.m.samples.number; j++){ for (j=0; j<this.m.samples.number; j++){
this.min[this.m.windows.length-1][j] = this.sum[j] this.min[this.m.clones.length-1][j] = this.sum[j]
this.sum[this.m.windows.length-1] += this.m.clone(this.m.windows.length-1).getSize(j) this.sum[this.m.clones.length-1] += this.m.clone(this.m.clones.length-1).getSize(j)
this.max[this.m.windows.length-1][j] = this.sum[j] this.max[this.m.clones.length-1][j] = this.sum[j]
} }
}, },
......
...@@ -60,7 +60,7 @@ List.prototype = { ...@@ -60,7 +60,7 @@ List.prototype = {
var div_list_clones = document.createElement('div') var div_list_clones = document.createElement('div')
div_list_clones.id = "list_clones" 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'); var div = document.createElement('li');
div.className = "list"; div.className = "list";
div.id = i; div.id = i;
...@@ -158,7 +158,7 @@ List.prototype = { ...@@ -158,7 +158,7 @@ List.prototype = {
var startTime = new Date() var startTime = new Date()
.getTime(); .getTime();
var elapsedTime = 0; 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]); this.updateElem([i]);
} }
elapsedTime = new Date() elapsedTime = new Date()
...@@ -472,7 +472,7 @@ List.prototype = { ...@@ -472,7 +472,7 @@ List.prototype = {
}, },
reset_filter: function (bool) { 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) var c = this.m.clone(i)
c.isFiltered=bool c.isFiltered=bool
} }
...@@ -480,7 +480,7 @@ List.prototype = { ...@@ -480,7 +480,7 @@ List.prototype = {
filter: function (str) { filter: function (str) {
this.reset_filter(true) 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) var c = this.m.clone(i)
if (c.getName().toUpperCase().indexOf(str.toUpperCase())!=-1 ) c.isFiltered = false if (c.getName().toUpperCase().indexOf(str.toUpperCase())!=-1 ) c.isFiltered = false
if (c.getSequence().toUpperCase().indexOf(str.toUpperCase())!=-1 ) c.isFiltered = false if (c.getSequence().toUpperCase().indexOf(str.toUpperCase())!=-1 ) c.isFiltered = false
......
This diff is collapsed.
...@@ -41,7 +41,7 @@ PDF.prototype = { ...@@ -41,7 +41,7 @@ PDF.prototype = {
if (this.list.length == 0) { if (this.list.length == 0) {
var flag = 5; 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) { if (this.m.clusters[i].length != 0 && flag != 0) {
this.list.push(i); this.list.push(i);
flag--; flag--;
...@@ -182,7 +182,7 @@ PDF.prototype = { ...@@ -182,7 +182,7 @@ PDF.prototype = {
opt2.y_offset = opt.y; opt2.y_offset = opt.y;
//clones style //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 polyline = elem.querySelectorAll('[id="polyline'+i+'"]')[0]
var color = tagColor[this.m.clone(i).getTag()] var color = tagColor[this.m.clone(i).getTag()]
...@@ -194,7 +194,7 @@ PDF.prototype = { ...@@ -194,7 +194,7 @@ PDF.prototype = {
polyline.setAttribute("stroke", color); 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); polyline.parentNode.removeChild(polyline);
} }
} }
...@@ -378,9 +378,9 @@ PDF.prototype = { ...@@ -378,9 +378,9 @@ PDF.prototype = {
this.doc.setFont('courier', 'normal'); this.doc.setFont('courier', 'normal');
this.doc.setTextColor(0, 0, 0) 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 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 seqN = seq.substring(this.m.clone(cloneID).Vend + 1, this.m.clone(cloneID).Jstart)
var seqJ = seq.substring(this.m.clone(cloneID).Jstart) var seqJ = seq.substring(this.m.clone(cloneID).Jstart)
...@@ -426,7 +426,7 @@ PDF.prototype = { ...@@ -426,7 +426,7 @@ PDF.prototype = {
} }
} else { } 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; this.y += 5;
...@@ -462,7 +462,7 @@ PDF.prototype = { ...@@ -462,7 +462,7 @@ PDF.prototype = {
icon: function (cloneID, x, y, w, h) { 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) var polyline = document.getElementById("polyline" + cloneID)
.cloneNode(true); .cloneNode(true);
......
...@@ -215,9 +215,9 @@ ScatterPlot.prototype = { ...@@ -215,9 +215,9 @@ ScatterPlot.prototype = {
this.grpLinks = this.plot_container.append('svg:g').attr('class', 'grpLinks'); this.grpLinks = this.plot_container.append('svg:g').attr('class', 'grpLinks');
//Initialisation des nodes //Initialisation des nodes
this.nodes = d3.range(this.m.n_windows) this.nodes = d3.range(this.m.n_clones)
.map(Object); .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].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].r1 = 5; // longueur du rayon1
this.nodes[i].r2 = 5; // longueur du rayon2 this.nodes[i].r2 = 5; // longueur du rayon2
...@@ -280,14 +280,14 @@ ScatterPlot.prototype = { ...@@ -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() { returnActiveclones: function() {
var activeWindows = 0; var activeclones = 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).isActive()) activeWindows += 1; if (this.m.clone(i).isActive()) activeclones += 1;
} }
return activeWindows; return activeclones;
}, },
/* Function which allows to initialize the D3JS engine - usefull with reinitMotor() /* Function which allows to initialize the D3JS engine - usefull with reinitMotor()
...@@ -682,7 +682,7 @@ ScatterPlot.prototype = { ...@@ -682,7 +682,7 @@ ScatterPlot.prototype = {
} }
//classement des clones suivant V //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()) { if (this.m.clone(i).isActive()) {
var geneV = this.m.clone(i).getV(); var geneV = this.m.clone(i).getV();
var clone = { var clone = {
...@@ -1135,7 +1135,7 @@ ScatterPlot.prototype = { ...@@ -1135,7 +1135,7 @@ ScatterPlot.prototype = {
/* Function which permits to force all no-clustered clones, to return at their initial position /* Function which permits to force all no-clustered clones, to return at their initial position
*/ */
forceNodesToStayInInitialPosition: function() { 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) { if (this.m.dbscan.clusters[this.m.clone(i).cluster].length == 1) {
//Calcul du delta //Calcul du delta
var x = this.nodes[i].x; var x = this.nodes[i].x;
......
...@@ -187,7 +187,7 @@ Segment.prototype = { ...@@ -187,7 +187,7 @@ Segment.prototype = {
* *
* */ * */
update: function () { 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]); this.updateElem([i]);
} }
}, },
......
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