From 6c1e59fb352488f3be970836e1b86250fd45f12f Mon Sep 17 00:00:00 2001
From: demetturan <demettrn@gmail.com>
Date: Thu, 10 Aug 2017 10:45:37 +0200
Subject: [PATCH] new tab is added to help section

---
 WebContent/data.xhtml           |  1 +
 WebContent/dataTable.xhtml      |  1 +
 WebContent/detailedSearch.xhtml |  1 +
 WebContent/graph.xhtml          |  1 +
 WebContent/help.xhtml           | 15 ++++++++++++---
 WebContent/information.xhtml    |  1 +
 WebContent/search.xhtml         | 27 ++++++++++++++++++---------
 7 files changed, 35 insertions(+), 12 deletions(-)

diff --git a/WebContent/data.xhtml b/WebContent/data.xhtml
index 3aaff29..422c64e 100644
--- a/WebContent/data.xhtml
+++ b/WebContent/data.xhtml
@@ -214,6 +214,7 @@ $(document).ready(function()
             <div class="col-sm-1">
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml" class="text-muted">Help</a></p>
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#documentation" class="text-sub">Documentation</a></p>
+              <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#sourceCode" class="text-sub">Source Code  &amp; Api</a></p>
               <p class="credit"><a href="/tabloidproteome/help.xhtml#contact" class="text-sub">Contact</a></p>
             </div>
           </div>
diff --git a/WebContent/dataTable.xhtml b/WebContent/dataTable.xhtml
index fa81a55..b70833d 100644
--- a/WebContent/dataTable.xhtml
+++ b/WebContent/dataTable.xhtml
@@ -542,6 +542,7 @@ body {
             <div class="col-sm-1">
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml" class="text-muted">Help</a></p>
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#documentation" class="text-sub">Documentation</a></p>
+              <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#sourceCode" class="text-sub">Source Code  &amp; Api</a></p>
               <p class="credit"><a href="/tabloidproteome/help.xhtml#contact" class="text-sub">Contact</a></p>
             </div>
           </div>
diff --git a/WebContent/detailedSearch.xhtml b/WebContent/detailedSearch.xhtml
index 450b622..f20b367 100644
--- a/WebContent/detailedSearch.xhtml
+++ b/WebContent/detailedSearch.xhtml
@@ -259,6 +259,7 @@ body {
             <div class="col-sm-1">
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml" class="text-muted">Help</a></p>
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#documentation" class="text-sub">Documentation</a></p>
+              <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#sourceCode" class="text-sub">Source Code  &amp; Api</a></p>
               <p class="credit"><a href="/tabloidproteome/help.xhtml#contact" class="text-sub">Contact</a></p>
             </div>
           </div>
diff --git a/WebContent/graph.xhtml b/WebContent/graph.xhtml
index a3b4047..4752f0d 100644
--- a/WebContent/graph.xhtml
+++ b/WebContent/graph.xhtml
@@ -676,6 +676,7 @@
             <div class="col-sm-1">
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml" class="text-muted">Help</a></p>
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#documentation" class="text-sub">Documentation</a></p>
+              <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#sourceCode" class="text-sub">Source Code  &amp; Api</a></p>
               <p class="credit"><a href="/tabloidproteome/help.xhtml#contact" class="text-sub">Contact</a></p>
             </div>
           </div>
diff --git a/WebContent/help.xhtml b/WebContent/help.xhtml
index 99bea71..5010e8e 100644
--- a/WebContent/help.xhtml
+++ b/WebContent/help.xhtml
@@ -107,6 +107,7 @@ $(document).ready(function()
         <div class="col-sm-3">
           <ul class="nav nav-pills brand-pills nav-stacked">
             <li class="active"><a href="#documentation" data-toggle="tab">Documentation</a></li>
+            <li><a href="#sourceCode" data-toggle="tab">Source Code &amp; Api</a></li>
             <li><a href="#contact" data-toggle="tab">Contact</a></li>
           </ul>
         </div>
@@ -116,9 +117,7 @@ $(document).ready(function()
               <p>Click 
               <a target="_blank" href="http://genesis.ugent.be/uvpublicdata/Tabloid_Proteome/TabloidProteome1.2_documentation.pdf">here </a>
               for documentation (pdf)</p>
-              <p>Click 
-              <a target="_blank" href="http://iomics.ugent.be/tabloidproteome/tabloidApi.html">here </a>
-              for api information</p>
+              
               <div>
                 <h3>Frequently Asked Questions</h3>
                 <div class="panel panel-default">
@@ -192,6 +191,15 @@ $(document).ready(function()
                 </div>
               </div>
             </div>
+            <div class="tab-pane" id="sourceCode">
+              <p>Source code is available on 
+              <a target="_blank" href="https://github.com/compomics/tabloidProteome">GitHub</a>
+              </p>
+              <p>Tabloid Proteome provides REST (Representational State Transfer) API which enables you to get the data without using the graphical user interface of the web page. 
+              This can be used to programmatically access some information without downloading entire dataset. Please click 
+              <a target="_blank" href="http://iomics.ugent.be/tabloidproteome/tabloidApi.html">here </a>
+              for api information</p>
+            </div>
             <div class="tab-pane" id="contact">
               <p>For any further questions, feedback or suggestions, you can send mail to one of the following person:</p>
               <p>Surya Gupta <a href="mailto:surya.gupta@vib-ugent.be" style="text-decoration: underline;">surya.gupta@vib-ugent.be</a></p>
@@ -260,6 +268,7 @@ $(document).ready(function()
             <div class="col-sm-1">
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml" class="text-muted">Help</a></p>
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#documentation" class="text-sub">Documentation</a></p>
+              <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#sourceCode" class="text-sub">Source Code &amp; Api</a></p>
               <p class="credit"><a href="/tabloidproteome/help.xhtml#contact" class="text-sub">Contact</a></p>
             </div>
           </div>
diff --git a/WebContent/information.xhtml b/WebContent/information.xhtml
index b6ea229..125ed2c 100644
--- a/WebContent/information.xhtml
+++ b/WebContent/information.xhtml
@@ -207,6 +207,7 @@ $(document).ready(function()
             <div class="col-sm-1">
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml" class="text-muted">Help</a></p>
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#documentation" class="text-sub">Documentation</a></p>
+              <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#sourceCode" class="text-sub">Source Code  &amp; Api</a></p>
               <p class="credit"><a href="/tabloidproteome/help.xhtml#contact" class="text-sub">Contact</a></p>
             </div>
           </div>
diff --git a/WebContent/search.xhtml b/WebContent/search.xhtml
index d99f700..ba454b4 100644
--- a/WebContent/search.xhtml
+++ b/WebContent/search.xhtml
@@ -69,10 +69,9 @@ body {
 	<script type="text/javascript">
 
 	function searchSingle(){
+
 		if($('#singleAccession').val() != ""){
-			if(($('#singleAccession').val().startsWith("P") &#124;&#124; $('#singleAccession').val().startsWith("O") &#124;&#124; 
-				$('#singleAccession').val().startsWith("Q") &#124;&#124; $('#singleAccession').val().startsWith("A")) 
-				&amp;&amp; $('#singleAccession').val().length == 6){
+			if(isValidUniprotAcc($('#singleAccession').val())){
 				window.location = '/tabloidproteome/dataTable.xhtml?accession='+ $('#singleAccession').val()
 	    		+ '&amp;jaccard=' + $('#jaccardSingle').val();
 		
@@ -106,12 +105,7 @@ body {
 	function searchDouble(){
 		if($('#doubleAccession1').val() != ""  &amp;&amp; $('#doubleAccession2').val() != "" ){
 			
-			if(($('#doubleAccession1').val().startsWith("P") &#124;&#124; $('#doubleAccession1').val().startsWith("Q")
-			&#124;&#124; $('#doubleAccession1').val().startsWith("O") &#124;&#124; $('#doubleAccession1').val().startsWith("A")) 
-			&amp;&amp; $('#doubleAccession1').val().length == 6
-			  &amp;&amp; ($('#doubleAccession2').val().startsWith("P") &#124;&#124; $('#doubleAccession2').val().startsWith("Q")
-			  &#124;&#124; $('#doubleAccession2').val().startsWith("O")&#124;&#124; $('#doubleAccession2').val().startsWith("A")) &amp;&amp; $('#doubleAccession2').val().length == 6
-			){
+			if(isValidUniprotAcc($('#doubleAccession1').val()) &amp;&amp; isValidUniprotAcc($('#doubleAccession2').val())){
 				window.location = '/tabloidproteome/dataTable.xhtml?accession1=' + $('#doubleAccession1').val()
 	        	+ '&amp;accession2=' + $('#doubleAccession2').val() + '&amp;jaccard=' + $('#jaccardDouble').val();
 		
@@ -144,6 +138,20 @@ body {
 		return false;
 	}
 	
+	function isValidUniprotAcc(accession){
+		if (accession.trim() == "") {
+            return false;
+        }
+        if (accession.length != 6 &amp;&amp; accession.length != 10) {
+        	return false;
+        }
+        var r = new RegExp("[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}", "i");
+        if(accession.match(r)){
+        	return true;
+        }
+        return false;
+	}
+	
 	function searchMultipleProtein(){
 		var array1 = [];
 		var array2 = [];
@@ -984,6 +992,7 @@ body {
             <div class="col-sm-1">
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml" class="text-muted">Help</a></p>
               <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#documentation" class="text-sub">Documentation</a></p>
+              <p class="credit" style="margin-bottom: 15px;"><a href="/tabloidproteome/help.xhtml#sourceCode" class="text-sub">Source Code &amp; Api</a></p>
               <p class="credit"><a href="/tabloidproteome/help.xhtml#contact" class="text-sub">Contact</a></p>
             </div>
           </div>