Merge branch 'master' of git+ssh://scm.gforge.inria.fr//gitroot/vidjil/vidjil

browser/css/dark.css

@@ -613,7 +613,7 @@ span .substitution {
   border-color: #333333;
 }
 #file_menu,
-#analysis_menu {
+#axis_choice {
   z-index: 2;
   border: solid;
   position: fixed;
@@ -896,7 +896,7 @@ span.logo {
 #file_menu,
 #tagSelector,
 .closeButton,
-#analysis_menu {
+#axis_choice {
   border-color: #333333;
 }
 #info_window td {

browser/css/light.css

@@ -613,7 +613,7 @@ span .substitution {
   border-color: #cccccc;
 }
 #file_menu,
-#analysis_menu {
+#axis_choice {
   z-index: 2;
   border: solid;
   position: fixed;
@@ -896,7 +896,7 @@ span.logo {
 #file_menu,
 #tagSelector,
 .closeButton,
-#analysis_menu {
+#axis_choice {
   border-color: #cccccc;
 }
 #info_window td {

browser/css/vidjil.less

@@ -743,7 +743,7 @@ span .substitution{
     border-color:@border;
 }
 
-#file_menu, #analysis_menu{
+#file_menu, #axis_choice{
   z-index:2;
   border:solid; 
   position: fixed; 
@@ -1035,7 +1035,7 @@ span.logo
   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; 
 }

browser/index.html

@@ -103,14 +103,14 @@
             m.load('upload_json','upload_pref', 200)">start</button> 
         </div>
 
-        <div id="analysis_menu" >
+        <div id="axis_choice" >
             <span class="closeButton" onclick="cancel();">X</span>
             <h2>analysis menu</h2>
 
             Analysis file:<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> 
         </div>
         
@@ -142,7 +142,7 @@
                         <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.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 class="menu_box">
                         <div id="upload_list">
@@ -218,8 +218,9 @@
 
                     <div class="menu_box">
                         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('rescale')" ><input type="radio" name="normalize_method" value="rescale" >rescale</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('to-100')" ><input type="radio" name="normalize_method" value="to-100">to 100%</input></div>
+
                     </div>
 
                     <div class="menu_box">

browser/js/builder.js

@@ -133,7 +133,7 @@ Builder.prototype = {
                 input.name = "normalize_list"
                 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")
                 div.onclick = function () {
@@ -158,7 +158,7 @@ Builder.prototype = {
                 input.name = "normalize_list"
                 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")
                 div.onclick = function () {

browser/js/menu.js

@@ -31,19 +31,19 @@ function loadData() {
     
     document.getElementById("file_menu")
         .style.display = "block";
-    document.getElementById("analysis_menu")
+    document.getElementById("axis_choice")
         .style.display = "none";
 }
 
 function loadAnalysis() {
-    document.getElementById("analysis_menu")
+    document.getElementById("axis_choice")
         .style.display = "block";
     document.getElementById("file_menu")
         .style.display = "none";
 }
 
 function cancel() {
-    document.getElementById("analysis_menu")
+    document.getElementById("axis_choice")
         .style.display = "none";
     document.getElementById("file_menu")
         .style.display = "none";

browser/js/model.js

@@ -76,7 +76,7 @@ Model.prototype = {
         
         this.norm = false;
         this.normalization = { 
-            "method" : "quantitative",
+            "method" : "constant",
             "A" : [],
             "B" : 0,
             "id" : -1
@@ -741,7 +741,7 @@ Model.prototype = {
             var A = this.normalization.A[time] /* standard/spike at point time */
             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
             }else{
                 normalized_size = B + ( (original_size - A) * ( (1 - B) / (1 - A) ) )
@@ -1569,7 +1569,7 @@ Model.prototype = {
         //header
         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 += ",size_"+i
+        for (var i=0; i<this.samples.order.length; i++) csv += ",ratio_"+i
         csv += "\n"
         
         //only non-empty active clones and "other"

server/web2py/applications/vidjil/views/patient/index.html

 {{extend 'db_layout.html'}}
 {{import vidjil_utils}}
 
-<h3>Patient list</h3>
+<h3></h3>
 
 <div class="db_block">
-    <div class="db_block_right">
+    <div class="db_block_left">
         search
         <input id="db_filter_input" type="text" value="{{=request.vars["filter"]}}"  onchange="db.call('patient/index', {'filter' : this.value} )">
     </div>