X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=3b10c142ebd2a233fd60f35a61971c2cf7830701;hb=e280466ffa0b7103da4a8ebe85aacbad354fd278;hp=9350c4b4a10f3fb19a7bc19a7cd9208abcb12722;hpb=66830878ef77fb7030de00ab6e302ef9936f0a3b;p=jalview.git

diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 9350c4b..3b10c14 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -80,7 +80,11 @@ function mcancelclosetime()
 document.onclick = mclose; 
 // -->
 </script>
-
+<script>
+<!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+</script> 
 </head>
 
 
@@ -88,10 +92,10 @@ document.onclick = mclose;
 
 
 <div id="header">
-<div id="logo"><a href="/" title="Home"></a></div>
+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
 <ul id="buttons">
 <li id="applet"><a href="applets.html" title="applet"></a></li>
-<li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
+<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
 </ul>
 </div>
 
@@ -100,39 +104,38 @@ document.onclick = mclose;
 <div id="navInner">
 
 <ul id="sddm">
- <li><a href="#">Home</a></li>
- <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
   <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Documentation</a>
-  <a href="#">Publications</a>
-  <a href="#">Credits</a>
-  <a href="#">Screenshots</a>
+  <a href="http://www.jalview.org/about/documentation">Documentation</a>
+  <a href="http://www.jalview.org/about/citation">Publications</a>
+  <a href="http://www.jalview.org/about/credits">Credits</a>
   </div>
  </li>
- <li><a href="#">FAQ</a></li>
- <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
   <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">News Mailing List</a>
-  <a href="#">Discussion Mailing List</a>
-  <a href="#">Links</a>
-  <a href="#">Community News</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+  <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+  <a href="http://www.jalview.org/community/links">Links</a>
+  <a href="http://www.jalview.org/community/community-news">Community News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
   <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Release History</a>
-  <a href="#">Jalview Bug Tracker</a>
-  <a href="#">Jalview Git Web</a>
-  <a href="#">Development News</a>
+  <a href="http://www.jalview.org/development/release-history">Release History</a>
+  <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+  <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+  <a href="http://www.jalview.org/development/development-news">Development News</a>
   </div>
  </li>
- <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
   <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
-  <a href="#">Training Courses</a>
-  <a href="#">Training News</a>
+  <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+  <a href="http://www.jalview.org/training/training-news">Training News</a>
   </div>
  </li>
- <li><a href="#" class="download-right">Download</a></li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 </ul>
 <div style="clear:both"></div>
 </div>
@@ -546,7 +549,7 @@ document.onclick = mclose;
           </li>
           <li>Note parameter &quot;PDBSeq&quot; is no longer required.<br>
           </li>
-          <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="../versions.html">versions archive if you want to download the old Jmol applet</a>.</li> 
+          <li>Jalview 2.3 was updated to work with Jmol 11. See the <a href="/development">versions archive if you want to download the old Jmol applet</a>.</li> 
             <p>&nbsp;</p>
           </li>
         </ul>
@@ -582,10 +585,10 @@ document.onclick = mclose;
         </ul>
         
 </div>
-
+</div>
 <div id ="footer">
 <div id="innerFooter">
-<div id="copyright"><p>Copyright all rights reserved 2012</p></div>
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
 <div id="cite">
 <p>
 If you use Jalview in your work, please cite this publication:
@@ -594,7 +597,7 @@ If you use Jalview in your work, please cite this publication:
 <p>
 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
-Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
 </p>
 </div>
 </div>