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Commit 8a1f3c30 authored by Marc Duez's avatar Marc Duez
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segmenter.js : segmenter can update sequence color/position whithout align reset 

-sequences are aligned using their windows (instead of Vstart)
parent 88e028ec
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browser/js/segmenter.js
View file @ 8a1f3c30
......@@ -37,6 +37,8 @@ function Segment(id, model, cgi_address) {
this.m.view.push(this); //synchronisation au Model
this.starPath = "M 0,6.1176482 5.5244193, 5.5368104 8.0000008,0 10.172535,5.5368104 16,6.1176482 11.406183,9.9581144 12.947371,16 8.0000008,12.689863 3.0526285,16 4.4675491,10.033876 z"
this.cgi_address = cgi_address
this.sequence = {};
}
......@@ -166,6 +168,9 @@ Segment.prototype = {
if (document.getElementById("seq" + list[i])) {
var spanF = document.getElementById("f" + list[i]);
this.div_elem(spanF, list[i]);
var spanM = document.getElementById("m" + list[i]);
spanM.innerHTML = this.sequence[list[i]].toString()
} else {
this.addToSegmenter(list[i]);
this.show();
......@@ -235,6 +240,8 @@ Segment.prototype = {
addToSegmenter: function (cloneID) {
var self = this;
this.sequence[cloneID] = new Sequence(cloneID, this.m)
var divParent = document.getElementById("listSeq");
var li = document.createElement('li');
li.id = "seq" + cloneID;
......@@ -247,45 +254,15 @@ Segment.prototype = {
spanF.id = "f" + cloneID;
this.div_elem(spanF, cloneID);
var spanM = this.buildSequence(cloneID)
li.appendChild(spanF);
li.appendChild(spanM);
divParent.appendChild(li);
},
buildSequence: function (cloneID) {
var spanM = document.createElement('span');
spanM.id = "m" + cloneID;
spanM.className = "seq-mobil";
spanM.innerHTML = this.sequence[cloneID].load().toString()
if (typeof this.m.windows[cloneID].sequence != 'undefined' && this.m.windows[cloneID].sequence != 0) {
var v_length = this.m.windows[cloneID].Vend + 1;
var size_marge = 300 - v_length;
var marge = "";
if (size_marge > 0) {
for (var i = 0; i < size_marge; i++) marge += "&nbsp";
}
var seq = new Sequence(cloneID, this.m)
spanM.innerHTML = marge + seq.load()
.toString()
} else {
var size_marge = 320 - this.m.windows[cloneID].window.length;
var marge = "";
for (var i = 0; i < size_marge; i++) marge += "&nbsp";
var spanJunc = document.createElement('span');
spanJunc.innerHTML = marge + this.m.windows[cloneID].window;
spanM.appendChild(spanJunc);
}
li.appendChild(spanF);
li.appendChild(spanM);
divParent.appendChild(li);
return spanM
},
......@@ -311,8 +288,7 @@ Segment.prototype = {
.getElementsByTagName("li");
if (li.length > 0) {
var id = li[0].id.substr(3);
var mid = $("#m" + id + " span:first-child")
.width() - 250;
var mid = 999999
$("#segmenter")
.animate({
scrollLeft: mid
......@@ -321,7 +297,7 @@ Segment.prototype = {
},
align: function () {
var self = this
var list = this.m.getSelected()
var request = "";
memTab = list;
......@@ -341,7 +317,7 @@ Segment.prototype = {
data: request,
url: this.cgi_address + "align.cgi",
success: function (result) {
displayAjaxResult(result);
self.displayAjaxResult(result);
}
});
},
......@@ -373,48 +349,50 @@ Segment.prototype = {
}
return result
},
displayAjaxResult: function(file) {
} //fin prototype
var json = JSON.parse(file)
function displayAjaxResult(file) {
for (var i = 0; i < json.seq.length; i++) {
var json = JSON.parse(file)
// global container
var spanM = document.getElementById("m" + memTab[i]);
spanM.innerHTML = "";
for (var i = 0; i < json.seq.length; i++) {
// global container
var spanM = document.getElementById("m" + memTab[i]);
spanM.innerHTML = "";
if (typeof m.windows[memTab[i]].sequence != 'undefined' && m.windows[memTab[i]].sequence != 0) {
var seq = new Sequence(memTab[i], m)
var seq = this.sequence[memTab[i]]
spanM.innerHTML = seq.load(json.seq[i])
.diff(json.seq[0])
.toString()
} else {
var spanJunc = document.createElement('span');
spanJunc.innerHTML = json.seq[i];
spanM.appendChild(spanJunc);
}
}
}
} //fin prototype Segment
function Sequence(id, model) {
this.id = id; //clone ID
this.m = model; //Model utilisé
this.seq = [];
this.pos = [];
this.use_marge = true
}
Sequence.prototype = {
//load sequence from model or use given argument
load: function (str) {
if (typeof str !== 'undefined') this.use_marge = false
str = typeof str !== 'undefined' ? str : this.m.windows[this.id].sequence;
if (typeof this.m.windows[this.id].sequence == 'undefined' || this.m.windows[this.id].sequence == 0) {
str = this.m.windows[this.id].window
}
this.seq = str.split("")
this.computePos()
......@@ -445,43 +423,61 @@ Sequence.prototype = {
//return sequence completed with html tag
toString: function () {
var seg = this.m.windows[this.id]
var result = ""
if (typeof seg.sequence != 'undefined' && seg.sequence != 0) {
//find V, D, J position
var endV = this.pos[seg.Vend]
var startJ = this.pos[seg.Jstart]
if (typeof seg.Dstart != 'undefined' && typeof seg.Dend != 'undefined') {
var startD = this.pos[seg.Dstart]
var endD = this.pos[seg.Dend]
}
//find V, D, J position
var endV = this.pos[seg.Vend]
var startJ = this.pos[seg.Jstart]
if (typeof seg.Dstart != 'undefined' && typeof seg.Dend != 'undefined') {
var startD = this.pos[seg.Dstart]
var endD = this.pos[seg.Dend]
}
//V color
var vColor = "";
if (this.m.colorMethod == "V") vColor = "style='color : " + seg.colorV + "'";
//J color
var jColor = "";
if (this.m.colorMethod == "J") jColor = "style='color : " + seg.colorJ + "'";
//V color
var vColor = "";
if (this.m.colorMethod == "V") vColor = "style='color : " + seg.colorV + "'";
//window
var window_start = this.pos[seg.sequence.indexOf(seg.window)]
var window_end = this.pos[seg.sequence.indexOf(seg.window)+seg.window.length]
var window_width = "style='width : " +((window_end - window_start) * 0.7333) + "em'" //TODO fix char width
//add span VDJ
var result = "<span class='V' " + vColor + " >"
for (var i = 0; i < this.seq.length; i++) {
result += this.seq[i]
//J color
var jColor = "";
if (this.m.colorMethod == "J") jColor = "style='color : " + seg.colorJ + "'";
if (i == endV) result += "</span><span class ='N'>"
if (i == startD - 1) result += "</span><span class ='D'>"
if (i == endD) result += "</span><span class ='N'>"
if (i == startJ - 1) result += "</span><span class ='J' " + jColor + " >"
//window
var window_start = this.pos[seg.sequence.indexOf(seg.window)]
var window_end = this.pos[seg.sequence.indexOf(seg.window)+seg.window.length]
var window_width = "style='width : " +((window_end - window_start) * 0.7333) + "em'" //TODO fix char width
if (i== window_start-1) result += "<span class='window1'><span class='window2' " + window_width + " ></span></span>"
//add span VDJ
if (typeof seg.Vend != 'undefined') result += "<span class='V' " + vColor + " >"
else result += "<span>"
for (var i = 0; i < this.seq.length; i++) {
result += this.seq[i]
if (i == endV) result += "</span><span class ='N'>"
if (i == startD - 1) result += "</span><span class ='D'>"
if (i == endD) result += "</span><span class ='N'>"
if (i == startJ - 1) result += "</span><span class ='J' " + jColor + " >"
if (i== window_start-1) result += "<span class='window1'><span class='window2' " + window_width + " ></span></span>"
}
result += "</span>"
}else{
var window_start = 0
result += seg.window
}
result += "</span>"
return result
//marge
var marge = ""
if (this.use_marge){
marge += "<span>";
var size_marge = 300 - window_start;
if (size_marge > 0) {
for (var i = 0; i < size_marge; i++) marge += "&nbsp";
}
marge += "</span>"
}
return marge + result
},
......
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