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

Conflicts:
	browser/css/dark.css
	browser/css/light.css
	browser/css/vidjil.less

browser/css/dark.css

@@ -438,7 +438,7 @@ line {
   text-align: center;
   border: solid;
   border-width: 1px;
-  border-color: #FFF;
+  border-color: #000000;
   border-radius: 5px;
   margin: 0px 1px;
 }
@@ -446,6 +446,11 @@ line {
   background: #073642;
 }
 .infoBox-open {
+  margin: -1px;
+  border: solid;
+  border-width: 1px;
+  border-color: #000000;
+  border-radius: 5px;
   background: #333333;
 }
 .systemBox,
@@ -1364,7 +1369,8 @@ text.alert {
 }
 .flash_0,
 .flash_1,
-.flash_2 {
+.flash_2,
+.flash_3 {
   width: 350px;
   min-height: 20px;
   border: solid;
@@ -1383,7 +1389,8 @@ text.alert {
 }
 .log_0,
 .log_1,
-.log_2 {
+.log_2,
+.log_3 {
   width: auto;
   min-height: 20px;
   display: block;
@@ -1401,6 +1408,11 @@ text.alert {
 }
 .flash_2,
 .log_2 {
+  font-weight: bold;
+  background-color: #F2DEAE;
+}
+.flash_3,
+.log_3 {
   font-weight: bold;
   border-color: darkred;
   background-color: #F2DEDE;

browser/css/light.css

@@ -438,7 +438,7 @@ line {
   text-align: center;
   border: solid;
   border-width: 1px;
-  border-color: #FFF;
+  border-color: #ffffff;
   border-radius: 5px;
   margin: 0px 1px;
 }
@@ -446,6 +446,11 @@ line {
   background: #fdf6e3;
 }
 .infoBox-open {
+  margin: -1px;
+  border: solid;
+  border-width: 1px;
+  border-color: #ffffff;
+  border-radius: 5px;
   background: #cccccc;
 }
 .systemBox,
@@ -1364,7 +1369,8 @@ text.alert {
 }
 .flash_0,
 .flash_1,
-.flash_2 {
+.flash_2,
+.flash_3 {
   width: 350px;
   min-height: 20px;
   border: solid;
@@ -1383,7 +1389,8 @@ text.alert {
 }
 .log_0,
 .log_1,
-.log_2 {
+.log_2,
+.log_3 {
   width: auto;
   min-height: 20px;
   display: block;
@@ -1401,6 +1408,11 @@ text.alert {
 }
 .flash_2,
 .log_2 {
+  font-weight: bold;
+  background-color: #F2DEAE;
+}
+.flash_3,
+.log_3 {
   font-weight: bold;
   border-color: darkred;
   background-color: #F2DEDE;

browser/css/vidjil.less

@@ -550,7 +550,7 @@ line {
   text-align: center;
   border: solid;
   border-width: 1px;
-  border-color: #FFF;
+  border-color: @background;
   border-radius: 5px;
   margin: 0px 1px;
 }
@@ -558,6 +558,11 @@ line {
   background: @highlight;
 }
 .infoBox-open{
+  margin: -1px;
+  border: solid;
+  border-width: 1px;
+  border-color: @background;
+  border-radius: 5px;
   background: @border;
 }
 
@@ -1552,7 +1557,7 @@ text.alert { fill: red; }
     display: none;
 }
 
-.flash_0, .flash_1, .flash_2 {
+.flash_0, .flash_1, .flash_2, .flash_3 {
     width: 350px;
     min-height: 20px;
     border: solid;
@@ -1570,7 +1575,7 @@ text.alert { fill: red; }
     transition: background 1s linear;
 }
 
-.log_0, .log_1, .log_2 {
+.log_0, .log_1, .log_2, .log_3 {
     width: auto;
     min-height: 20px;
     display: block;
@@ -1588,6 +1593,11 @@ text.alert { fill: red; }
 }
 
 .flash_2, .log_2 {
+    font-weight: bold;
+    background-color: #F2DEAE;
+}
+
+.flash_3, .log_3 {
     font-weight: bold;
     border-color: darkred;
     background-color: #F2DEDE;

browser/js/clone.js

@@ -212,7 +212,7 @@ Clone.prototype = {
     getFasta: function() {
         fasta = ''
         fasta += '>' + this.getCode() + '    ' + this.getPrintableSize() + '\n'
-        fasta += this.getSequence() + '\n'
+        fasta += this.getPrintableSegSequence() + '\n'
 
         return fasta
     },
@@ -338,6 +338,22 @@ Clone.prototype = {
         }
     },
 
+    getPrintableSegSequence: function () {
+        if (typeof this.seg == 'undefined' || typeof this.seg['5end'] == 'undefined' || typeof this.seg['3start'] == 'undefined') {
+            return this.getSequence()
+        }
+
+        var s = ''
+        s += this.sequence.substring(0,  this.seg['5end'])
+        s += '\n'
+        if (this.seg['5end'] < this.seg['3start'] - 1) {
+            s += this.sequence.substring(this.seg['5end'], this.seg['3start'] - 1)
+            s += '\n'
+        }
+        s += this.sequence.substring(this.seg['3start'] - 1)
+        return s
+    },
+
     computeGCContent: function () {
         if (typeof (this.sequence) == 'undefined') {
             this.GCContent = '?'

browser/js/com.js

@@ -27,9 +27,14 @@
 function Com(default_console) {
     this.data_id = "data-container"; //TODO
     this.default = default_console;
+
+    this.DEBUG = 0
+    this.INFO = 1
+    this.WARN = 2
+    this.ERROR = 3
     
-    this.min_priority = 1; // minimum required to display message
-    this.min_priority_console = 0;
+    this.min_priority = this.INFO // minimum required to display message
+    this.min_priority_console = this.DEBUG
     this.build()
     
     BUTTON_CLOSE_POPUP = "</br></br> <div class='center' > <button onclick='console.closePopupMsg()'>ok</button></div> ",
@@ -181,7 +186,7 @@ Com.prototype = {
             }).appendTo(this.flash_container)
             .slideDown(200);
             
-            if (priority !=2){
+            if (priority < this.ERROR){
                 setTimeout(function(){
                     div.fadeOut('slow', function() { div.remove();});
                 }, 8000);

browser/js/database.js

@@ -188,10 +188,11 @@ Database.prototype = {
             m.parseJsonAnalysis(result)
             m.initClones()
         }
-        
-        //TODO server need to return message priority too ( 0=console, 1=ok, 2=error)
-        if (res.message) console.log({"type": "flash", "msg": "database : " + res.message , "priority": 1})
-        
+
+        // server message
+        if (res.message) console.log({"type": "flash",
+                                      "msg": "database : " + res.message,
+                                      "priority": res.success == "false" ? 2 : 1}) // res.success can be 'undefined'
         return res
 
         if (this.url.length == 1) $("#db_back").addClass("inactive");
@@ -425,7 +426,7 @@ Database.prototype = {
             },
             error: function (request, status, error) {
                 if (status === "timeout") {
-                    console.log({"type": "flash", "default" : "database_timeout", "msg" : " - unable to access patient data" , "priority": 1});
+                    console.log({"type": "flash", "default" : "database_timeout", "msg" : " - unable to access patient data" , "priority": 2});
                 } else {
                     console.log({"type": "popup", "msg": request.responseText});
                 }
@@ -482,7 +483,7 @@ Database.prototype = {
             error: function (request, status, error) {
                 self.m.resume()
                 if (status === "timeout") {
-                    console.log({"type": "flash", "default" : "database_timeout", "msg": " - unable to access patient data" , "priority": 1});
+                    console.log({"type": "flash", "default" : "database_timeout", "msg": " - unable to access patient data" , "priority": 2});
                 } else {
                     console.log({"type": "popup", "msg": request.responseText});
                 }
@@ -505,7 +506,7 @@ Database.prototype = {
             },
             error: function (request, status, error) {
                 if (status === "timeout") {
-                    console.log({"type": "flash", "default" : "database_timeout", "msg": " - unable to access patient data" , "priority": 1});
+                    console.log({"type": "flash", "default" : "database_timeout", "msg": " - unable to access patient data" , "priority": 2});
                 } else {
                     console.log({"type": "popup", "msg": request.responseText});
                 }