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Merge branch 'JAL-1422_srs' into Release_2_8_Branch
authorJim Procter <jprocter@compbio.dundee.ac.uk>
Mon, 13 Jan 2014 14:05:51 +0000 (14:05 +0000)
committerJim Procter <jprocter@compbio.dundee.ac.uk>
Mon, 13 Jan 2014 14:05:51 +0000 (14:05 +0000)
Conflicts:
examples/linkedapplets_ng.html

1  2 
examples/appletParameters.html patch | diff1 | diff2 | blob | history
examples/applets.html patch | diff1 | diff2 | blob | history
examples/embedded.html patch | diff1 | diff2 | blob | history
examples/embeddedWJmol.html patch | diff1 | diff2 | blob | history
examples/linkedapplets_ng.html patch | diff1 | diff2 | blob | history

diff --combined examples/appletParameters.html
index 4779046,af1ec87..5f7305d
--- 1/examples/appletParameters.html
--- 2/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@@ -80,11 -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>
  
  
@@@ -92,10 -88,10 +92,10 @@@
  
  
  <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>
  
@@@ -104,38 -100,39 +104,38 @@@
  <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>
@@@ -174,11 -171,6 +174,11 @@@
              <td width="80" ><strong>value=&quot;&quot;&gt;</strong></td>
              <td width="100%"><strong>Description</strong></td>
            </tr>
 +          <tr>
 +          <td>permissions</td>
 +          <td>sandbox</td>
 +          <td><strong>This parameter is necessary, and must have the value <em>sandbox</em> to allow the JalviewLite applet to run.</strong></td>
 +          </tr>
            <tr> 
              <td>file</td>
              <td>fileName</td>
@@@ -308,7 -300,7 +308,7 @@@
            </tr>
            <tr> 
              <td>linkLabel_1</td>
-             <td>Uniprot</td>
+             <td>EMBL-EBI Search</td>
              <td rowspan="2"><p>Right click on sequence id to see list of available 
                  links. Any new links MUST have $SEQUENCE_ID$ as part of the linkURL_n 
                  value. For multiple links, increment the label and url name by 
@@@ -321,12 -313,12 +321,12 @@@
                <br>Regex URL links are also applied to the description line (since Jalview 2.4.+).</em></p></td>
            </tr>
            <tr> 
-             <td> <p><br>
+             <td> <p>
+             <br>
                  linkUrl_1<br>
                </p></td>
              <td><p><br>
-                 http://us.expasy.org/cgi-bin/<br>
-                 niceprot.pl?$SEQUENCE_ID$</p>
+                 http://www.ebi.ac.uk/ebisearch/<br/>search.ebi?db=allebi&query=$SEQUENCE_ID$</p>
                                                </td>
            </tr>
            <tr> 
@@@ -554,7 -546,7 +554,7 @@@
            </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>
@@@ -607,5 -599,18 +607,5 @@@ Bioinformatics 25 (9) 1189-1191 <a href
  </div>
  </div>
  </div>
 -
 -<script type="text/javascript">
 -    var gaJsHost = (("https:" == document.location.protocol) ?
 - "https://ssl." : "http://www.");
 -    document.write(unescape("%3Cscript src=\'" + gaJsHost +
 - "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
 -</script>
 -<script type="text/javascript">
 -try{
 -    var pageTracker = _gat._getTracker("'UA-9060947-1'");
 -    pageTracker._trackPageview();
 -} catch(err) {}
 -</script>
  </body>
  </html>
diff --combined examples/applets.html
index 255f104,e88742e..0629af0
--- 1/examples/applets.html
--- 2/examples/applets.html
+++ b/examples/applets.html
@@@ -79,11 -79,7 +79,11 @@@ 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>
  
  
@@@ -91,10 -87,10 +91,10 @@@
  
  
  <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>
  
@@@ -103,38 -99,39 +103,38 @@@
  <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>
@@@ -178,7 -175,6 +178,7 @@@
        <td width="10%" valign="center"><applet
          code="jalview.bin.JalviewLite" width="140" height="35"
          archive="jalviewApplet.jar">
 +<param name="permissions" value="sandbox">
         <param name="file" value="uniref50.fa">
          <param name="treeFile" value="ferredoxin.nw">
           <param name="userDefinedColour"
@@@ -190,9 -186,9 +190,9 @@@
            <param name="linkLabel_1" value="Uniprot">
             <param name="linkUrl_1"
              value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
-             <param name="linkLabel_2" value="Expasy">
+             <param name="linkLabel_2" value="EMBL-EBI Search">
               <param name="linkUrl_2"
-               value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+               value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
         <param name="APPLICATION_URL"
          value="http://www.jalview.org/services/launchApp">
         </applet></td>
@@@ -204,7 -200,6 +204,7 @@@
        <td width="10%" valign="center"><applet
          code="jalview.bin.JalviewLite" width="140" height="35"
          archive="jalviewApplet.jar">
 +<param name="permissions" value="sandbox">
         <param name="file" value="uniref50.fa">
          <param name="features" value="exampleFeatures.txt">
           <param name="showFeatureSettings" value="true">
@@@ -216,10 -211,10 +216,10 @@@
         <param name="linkLabel_1" value="Uniprot">
          <param name="linkUrl_1"
           value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
-          <param name="linkLabel_2" value="Expasy">
-           <param name="linkUrl_2"
-            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
-            <param name="APPLICATION_URL"
+                      <param name="linkLabel_2" value="EMBL-EBI Search">
+              <param name="linkUrl_2"
+               value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
+         <param name="APPLICATION_URL"
              value="http://www.jalview.org/services/launchApp">
         </applet></td>
        <td valign="center">Displays a features file on the alignment</td>
@@@ -228,7 -223,6 +228,7 @@@
        <td width="10%" valign="center"><applet
          code="jalview.bin.JalviewLite" width="140" height="35"
          archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
 +<param name="permissions" value="sandbox">
         <param name="file" value="uniref50.fa">
          <!-- <param name="debug" value="true">
                          -->
@@@ -241,9 -235,9 +241,9 @@@
         <param name="linkLabel_1" value="Uniprot">
          <param name="linkUrl_1"
           value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
-          <param name="linkLabel_2" value="Expasy">
-           <param name="linkUrl_2"
-            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+             <param name="linkLabel_2" value="EMBL-EBI Search">
+              <param name="linkUrl_2"
+               value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
         <param name="APPLICATION_URL"
          value="http://www.jalview.org/services/launchApp">
          <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
@@@ -255,7 -249,6 +255,7 @@@
        <td width="10%" valign="middle"><applet
          code="jalview.bin.JalviewLite" width="140" height="35"
          archive="jalviewApplet.jar">
 +<param name="permissions" value="sandbox">
         <param name="file" value="jpred_msa.fasta">
          <param name="jnetfile" value="jpred_msa.seq.concise">
           <param name="defaultColour" value="Clustal">
@@@ -269,9 -262,9 +269,9 @@@
         <param name="linkLabel_1" value="Uniprot">
          <param name="linkUrl_1"
           value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
-          <param name="linkLabel_2" value="Expasy">
-           <param name="linkUrl_2"
-            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+             <param name="linkLabel_2" value="EMBL-EBI Search">
+              <param name="linkUrl_2"
+               value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
         <param name="APPLICATION_URL"
          value="http://www.jalview.org/services/launchApp">
         </applet></td>
@@@ -288,7 -281,6 +288,7 @@@
        <td width="10%" valign="center"><applet
          code="jalview.bin.JalviewLite" width="140" height="35"
          archive="jalviewApplet.jar">
 +<param name="permissions" value="sandbox">
         <param name="file" value="RF00031_folded.stk">
          <param name="defaultColour" value="Purine/Pyrimidine">
           <param name="showAnnotation" value="true">
@@@ -327,4 -319,4 +327,4 @@@ Bioinformatics 25 (9) 1189-1191 <a href
  </div>
  </body>
  </html>
 -          
 +          
diff --combined examples/embedded.html
index eda8a27,b9d26cb..ce6fca5
--- 1/examples/embedded.html
--- 2/examples/embedded.html
+++ b/examples/embedded.html
@@@ -79,11 -79,7 +79,11 @@@ 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>
  
  
@@@ -91,10 -87,10 +91,10 @@@
  
  
  <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>
  
@@@ -103,38 -99,39 +103,38 @@@
  <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>
@@@ -169,8 -166,7 +169,8 @@@
  </ul>
  <applet code="jalview.bin.JalviewLite"
                        width="756" height="560" archive="jalviewApplet.jar">
 -                      <param name="file" value="plantfdx.fa">
 +                      <param name="permissions" value="sandbox">
 +      <param name="file" value="plantfdx.fa">
                        <param name="annotations" value="plantfdx.annotations">
                        <param name="features" value="plantfdx.features">
                        <param name="embedded" value="true">
@@@ -180,9 -176,9 +180,9 @@@
         <param name="linkLabel_1" value="Uniprot">
          <param name="linkUrl_1"
           value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
-          <param name="linkLabel_2" value="Expasy">
-           <param name="linkUrl_2"
-            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+             <param name="linkLabel_2" value="EMBL-EBI Search">
+              <param name="linkUrl_2"
+               value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
                        <param name="APPLICATION_URL"
                                value="http://www.jalview.org/services/launchApp">
                </applet>
diff --combined examples/embeddedWJmol.html
index 24f7406,a3a7c3d..af15654
--- 1/examples/embeddedWJmol.html
--- 2/examples/embeddedWJmol.html
+++ b/examples/embeddedWJmol.html
@@@ -19,11 -19,6 +19,11 @@@
  <html xmlns="http://www.w3.org/1999/xhtml">
  <head>
  <TITLE>Embedded JalviewLite talking to externally managed Jmol</TITLE>
 +<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="javascript/deployJava.js"></script>
  <script src="jmol/Jmol.js"></script>
  <script src="javascript/jquery-1.4.4.min.js"></script>
@@@ -101,15 -96,14 +101,15 @@@ function genHref(
    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/$SEQUENCE_ID$",
    APPLICATION_URL : "http://www.jalview.org/services/launchApp",
 -  PDBfile : "1gaq.txt FER1_MAIZE"
 +  PDBfile : "1gaq.txt FER1_MAIZE",
 +  permissions : "sandbox"
   };
   jmolSetCallback("hoverCallback","_jmolhover");
    jmolSetCallback("pickCallback","_jmolpick");
@@@ -183,10 -177,10 +183,10 @@@ 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>
  
@@@ -195,38 -189,39 +195,38 @@@
  <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>
@@@ -274,5 -269,18 +274,5 @@@ Bioinformatics 25 (9) 1189-1191 <a href
  </div>
  </div>
  </div>
 -
 -<script type="text/javascript">
 -    var gaJsHost = (("https:" == document.location.protocol) ?
 - "https://ssl." : "http://www.");
 -    document.write(unescape("%3Cscript src=\'" + gaJsHost +
 - "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
 -</script>
 -<script type="text/javascript">
 -try{
 -    var pageTracker = _gat._getTracker("'UA-9060947-1'");
 -    pageTracker._trackPageview();
 -} catch(err) {}
 -</script>
  </body>
  </html>
diff --combined examples/linkedapplets_ng.html
index ef43184,3418068..c36f649
--- 1/examples/linkedapplets_ng.html
--- 2/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@@ -23,11 -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";
@@@ -111,10 -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>
  
@@@ -123,38 -118,39 +123,38 @@@
  <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>
@@@ -200,15 -196,12 +200,13 @@@
      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?$SEQUENCE_ID$",
 +    permissions : 'sandbox',
+     linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
      APPLICATION_URL : "http://www.jalview.org/services/launchApp"
    };
   
@@@ -235,16 -228,13 +233,14 @@@
      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?$SEQUENCE_ID$",
 +    permissions : 'sandbox',
-     APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+     linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+    APPLICATION_URL : "http://www.jalview.org/services/launchApp"
    };
    deployJava.runApplet(attributes, parameters, '1.6');
  </script>
@@@ -273,5 -263,18 +269,5 @@@ Bioinformatics 25 (9) 1189-1191 <a href
  </div>
  </div>
  </div>
 -
 -<script type="text/javascript">
 -    var gaJsHost = (("https:" == document.location.protocol) ?
 - "https://ssl." : "http://www.");
 -    document.write(unescape("%3Cscript src=\'" + gaJsHost +
 - "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
 -</script>
 -<script type="text/javascript">
 -try{
 -    var pageTracker = _gat._getTracker("'UA-9060947-1'");
 -    pageTracker._trackPageview();
 -} catch(err) {}
 -</script>
  </body>
  </html>