Commit 61690c60 authored by Marc Duez's avatar Marc Duez
Browse files
parents 773992d5 d366ba02
...@@ -613,7 +613,7 @@ span .substitution { ...@@ -613,7 +613,7 @@ span .substitution {
border-color: #333333; border-color: #333333;
} }
#file_menu, #file_menu,
#analysis_menu { #axis_choice {
z-index: 2; z-index: 2;
border: solid; border: solid;
position: fixed; position: fixed;
...@@ -896,7 +896,7 @@ span.logo { ...@@ -896,7 +896,7 @@ span.logo {
#file_menu, #file_menu,
#tagSelector, #tagSelector,
.closeButton, .closeButton,
#analysis_menu { #axis_choice {
border-color: #333333; border-color: #333333;
} }
#info_window td { #info_window td {
......
...@@ -613,7 +613,7 @@ span .substitution { ...@@ -613,7 +613,7 @@ span .substitution {
border-color: #cccccc; border-color: #cccccc;
} }
#file_menu, #file_menu,
#analysis_menu { #axis_choice {
z-index: 2; z-index: 2;
border: solid; border: solid;
position: fixed; position: fixed;
...@@ -896,7 +896,7 @@ span.logo { ...@@ -896,7 +896,7 @@ span.logo {
#file_menu, #file_menu,
#tagSelector, #tagSelector,
.closeButton, .closeButton,
#analysis_menu { #axis_choice {
border-color: #cccccc; border-color: #cccccc;
} }
#info_window td { #info_window td {
......
...@@ -743,7 +743,7 @@ span .substitution{ ...@@ -743,7 +743,7 @@ span .substitution{
border-color:@border; border-color:@border;
} }
#file_menu, #analysis_menu{ #file_menu, #axis_choice{
z-index:2; z-index:2;
border:solid; border:solid;
position: fixed; position: fixed;
...@@ -1035,7 +1035,7 @@ span.logo ...@@ -1035,7 +1035,7 @@ span.logo
color: grey; color: grey;
} }
.selector, #list_menu, #top-container, .list_clones, .bot-bar, #bot-container, #popup-container, #file_menu, #tagSelector, .closeButton, #analysis_menu .selector, #list_menu, #top-container, .list_clones, .bot-bar, #bot-container, #popup-container, #file_menu, #tagSelector, .closeButton, #axis_choice
{ {
border-color: @border; border-color: @border;
} }
......
...@@ -103,14 +103,14 @@ ...@@ -103,14 +103,14 @@
m.load('upload_json','upload_pref', 200)">start</button> m.load('upload_json','upload_pref', 200)">start</button>
</div> </div>
<div id="analysis_menu" > <div id="axis_choice" >
<span class="closeButton" onclick="cancel();">X</span> <span class="closeButton" onclick="cancel();">X</span>
<h2>analysis menu</h2> <h2>analysis menu</h2>
Analysis file:<br/> Analysis file:<br/>
<input id="upload_analysis" type="file" name="analysis" /></br></br> <input id="upload_analysis" type="file" name="analysis" /></br></br>
<button onclick="document.getElementById('analysis_menu').style.display='none'; <button onclick="document.getElementById('axis_choice').style.display='none';
m.loadAnalysis('upload_analysis');">start</button> m.loadAnalysis('upload_analysis');">start</button>
</div> </div>
...@@ -142,7 +142,7 @@ ...@@ -142,7 +142,7 @@
<a class="buttonSelector" onclick="javascript:m.saveAnalysis()">export analysis</a> <a class="buttonSelector" onclick="javascript:m.saveAnalysis()">export analysis</a>
<a class="buttonSelector" onclick="javascript:pdf.make()">export pdf (graph + selected clones)</a> <a class="buttonSelector" onclick="javascript:pdf.make()">export pdf (graph + selected clones)</a>
<a class="buttonSelector" onclick="javascript:pdf.makeGraph()">export pdf (graph)</a> <a class="buttonSelector" onclick="javascript:pdf.makeGraph()">export pdf (graph)</a>
<a class="buttonSelector" onclick="javascript:m.exportCSV()">export CSV</a> <a class="buttonSelector" onclick="javascript:m.exportCSV()">export csv (visible clones)</a>
</div> </div>
<div class="menu_box"> <div class="menu_box">
<div id="upload_list"> <div id="upload_list">
...@@ -218,8 +218,9 @@ ...@@ -218,8 +218,9 @@
<div class="menu_box"> <div class="menu_box">
normalization method</br> normalization method</br>
<div class="buttonSelector" onclick="m.changeNormMethod('quantitative')" ><input type="radio" name="normalize_method" value="quantitative" checked>quantitative</input></div> <div class="buttonSelector" onclick="m.changeNormMethod('constant')" ><input type="radio" name="normalize_method" value="constant" checked >constant</input></div>
<div class="buttonSelector" onclick="m.changeNormMethod('rescale')" ><input type="radio" name="normalize_method" value="rescale" >rescale</input></div> <div class="buttonSelector" onclick="m.changeNormMethod('to-100')" ><input type="radio" name="normalize_method" value="to-100">to 100%</input></div>
</div> </div>
<div class="menu_box"> <div class="menu_box">
......
...@@ -133,7 +133,7 @@ Builder.prototype = { ...@@ -133,7 +133,7 @@ Builder.prototype = {
input.name = "normalize_list" input.name = "normalize_list"
if (self.m.normalization.id==i) input.checked=true; if (self.m.normalization.id==i) input.checked=true;
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)
var div = document.createElement("div") var div = document.createElement("div")
div.onclick = function () { div.onclick = function () {
...@@ -158,7 +158,7 @@ Builder.prototype = { ...@@ -158,7 +158,7 @@ Builder.prototype = {
input.name = "normalize_list" input.name = "normalize_list"
if (self.m.normalization.id==key) input.checked=true; if (self.m.normalization.id==key) input.checked=true;
var text = document.createTextNode(key + " => " +self.m.data[key].expected) var text = document.createTextNode(key + " " +self.m.data[key].expected)
var div = document.createElement("div") var div = document.createElement("div")
div.onclick = function () { div.onclick = function () {
......
...@@ -31,19 +31,19 @@ function loadData() { ...@@ -31,19 +31,19 @@ function loadData() {
document.getElementById("file_menu") document.getElementById("file_menu")
.style.display = "block"; .style.display = "block";
document.getElementById("analysis_menu") document.getElementById("axis_choice")
.style.display = "none"; .style.display = "none";
} }
function loadAnalysis() { function loadAnalysis() {
document.getElementById("analysis_menu") document.getElementById("axis_choice")
.style.display = "block"; .style.display = "block";
document.getElementById("file_menu") document.getElementById("file_menu")
.style.display = "none"; .style.display = "none";
} }
function cancel() { function cancel() {
document.getElementById("analysis_menu") document.getElementById("axis_choice")
.style.display = "none"; .style.display = "none";
document.getElementById("file_menu") document.getElementById("file_menu")
.style.display = "none"; .style.display = "none";
......
...@@ -76,7 +76,7 @@ Model.prototype = { ...@@ -76,7 +76,7 @@ Model.prototype = {
this.norm = false; this.norm = false;
this.normalization = { this.normalization = {
"method" : "quantitative", "method" : "constant",
"A" : [], "A" : [],
"B" : 0, "B" : 0,
"id" : -1 "id" : -1
...@@ -741,7 +741,7 @@ Model.prototype = { ...@@ -741,7 +741,7 @@ Model.prototype = {
var A = this.normalization.A[time] /* standard/spike at point time */ var A = this.normalization.A[time] /* standard/spike at point time */
var B = this.normalization.B /* standard/spike expected value */ var B = this.normalization.B /* standard/spike expected value */
if (this.normalization.method=="rescale" || original_size <= A){ if (this.normalization.method=="constant" || original_size <= A){
normalized_size = (original_size * B) / A normalized_size = (original_size * B) / A
}else{ }else{
normalized_size = B + ( (original_size - A) * ( (1 - B) / (1 - A) ) ) normalized_size = B + ( (original_size - A) * ( (1 - B) / (1 - A) ) )
...@@ -1569,7 +1569,7 @@ Model.prototype = { ...@@ -1569,7 +1569,7 @@ Model.prototype = {
//header //header
var csv = "name,id,system,tag,v,d,j,sequence" var csv = "name,id,system,tag,v,d,j,sequence"
for (var i=0; i<this.samples.order.length; i++) csv += ",reads_"+i for (var i=0; i<this.samples.order.length; i++) csv += ",reads_"+i
for (var i=0; i<this.samples.order.length; i++) csv += ",size_"+i for (var i=0; i<this.samples.order.length; i++) csv += ",ratio_"+i
csv += "\n" csv += "\n"
//only non-empty active clones and "other" //only non-empty active clones and "other"
......
{{extend 'db_layout.html'}} {{extend 'db_layout.html'}}
{{import vidjil_utils}} {{import vidjil_utils}}
<h3>Patient list</h3> <h3></h3>
<div class="db_block"> <div class="db_block">
<div class="db_block_right"> <div class="db_block_left">
search search
<input id="db_filter_input" type="text" value="{{=request.vars["filter"]}}" onchange="db.call('patient/index', {'filter' : this.value} )"> <input id="db_filter_input" type="text" value="{{=request.vars["filter"]}}" onchange="db.call('patient/index', {'filter' : this.value} )">
</div> </div>
......
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