X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Flinkedapplets_ng.html;h=1d6b4471987d9ffb9d33cb13ad73f6090f37ded7;hb=4e46768e658aa0fe03668556d8b81f930c99c457;hp=80bda5e2fe4b9da2b23d2f6d500c2889d5ae26ad;hpb=92d3ddd8e9cf6f34759557f3ed85a12a1dd91c34;p=jalview.git

diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index 80bda5e..1d6b447 100644
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -23,6 +23,11 @@
   
  <link href="css/reset.css" rel="stylesheet" type="text/css" />
  <link href="css/style.css" rel="stylesheet" type="text/css" />
+<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>
 <script src="http://www.java.com/js/deployJava.js"></script>
 <script src="javascript/jalview.js" language="javascript"></script>
 <script>  //deployJava.debug="true";
@@ -106,10 +111,10 @@ 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>
 
@@ -118,39 +123,38 @@ 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>
@@ -167,7 +171,7 @@ document.onclick = mclose;
 <li><a href="jalviewLiteJs.html">Javascript API</a></li>
 <li><a href="formComplete.html">in-page API demo</a></li>
 <li class="jvlite-nav-small"><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
-<li><a href="embeddedWJmol.html">Sequence And Structure demo</a></li>
+<li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
 </ul>
 </div>
 
@@ -175,13 +179,6 @@ document.onclick = mclose;
     <strong>JalviewLite Linked Applets Demo<br></strong>
     <p>The two applets below use <a href="JalviewLiteJs.html">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
     </p>
-    <p>See the other demonstration pages below to see the API in action:</p>
-    <ul>
-          <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>
-          <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page.</a></li>
-          <li><a href="javascriptLaunch.html">launch JalviewLite from a javascript button</a></li>
-          
-    </ul>
 	<script> 
   var attributes = {
     code : 'jalview.bin.JalviewLite',
@@ -203,18 +200,17 @@ document.onclick = mclose;
     embedded : "true",
     showFullId : "false",
     RGB : "F2F2FF",
-    linkLabel_1 : "SRS",
-    linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
- 
+    linkLabel_1 : "EMBL-EBI Search",
+    linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
     ,
     linkLabel_2 : "Uniprot"
- 
     ,
-    linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
+    linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+    permissions : 'sandbox',
     APPLICATION_URL : "http://www.jalview.org/services/launchApp"
   };
  
-  deployJava.runApplet(attributes, parameters, '1.6');
+  deployJava.runApplet(attributes, parameters, '1.6+');
 </script>
 <script> 
   var attributes = {
@@ -237,17 +233,16 @@ document.onclick = mclose;
     embedded : "true",
     showFullId : "false",
     RGB : "F2F2FF",
-    linkLabel_1 : "SRS",
-    linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
- 
+    linkLabel_1 : "EMBL-EBI Search",
+    linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
     ,
     linkLabel_2 : "Uniprot"
- 
     ,
-    linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
-    APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+    linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+    permissions : 'sandbox',
+   APPLICATION_URL : "http://www.jalview.org/services/launchApp"
   };
-  deployJava.runApplet(attributes, parameters, '1.6');
+  deployJava.runApplet(attributes, parameters, '1.6+');
 </script>
     <p>
 <!--      <a href="javascript:linkJvJmol()">Click Me If you don't see any messages below</a>
@@ -256,6 +251,23 @@ document.onclick = mclose;
         id="stdout" rows="20" cols="80">Messages  will appear here.</textarea></form>
       <br>
 </p>
-
+</div>
+</div>
+<div id ="footer">
+<div id="innerFooter">
+<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:
+</p>
+<br />
+<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 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
+</div>
 </body>
 </html>