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Merge branch 'Release_2_8_Branch' into WIP_fix_JAL-1423
[jalview.git] / examples / applets.html
diff --git a/examples/applets.html b/examples/applets.html
index e3e1d3c..a6d61f8 100755 (executable)
--- a/examples/applets.html
+++ b/examples/applets.html
@@ -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>
 
 
@@ -87,10 +91,10 @@ 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>
 
@@ -99,39 +103,38 @@ 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>
@@ -175,6 +178,7 @@ document.onclick = mclose;
       <td width="10%" valign="center"><applet
         code="jalview.bin.JalviewLite" width="140" height="35"
         archive="jalviewApplet.jar">
+<param name="permissions" value="all-permissions">
        <param name="file" value="uniref50.fa">
         <param name="treeFile" value="ferredoxin.nw">
          <param name="userDefinedColour"
@@ -186,9 +190,9 @@ document.onclick = mclose;
           <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>
@@ -200,6 +204,7 @@ document.onclick = mclose;
       <td width="10%" valign="center"><applet
         code="jalview.bin.JalviewLite" width="140" height="35"
         archive="jalviewApplet.jar">
+<param name="permissions" value="all-permissions">
        <param name="file" value="uniref50.fa">
         <param name="features" value="exampleFeatures.txt">
          <param name="showFeatureSettings" value="true">
@@ -211,10 +216,10 @@ document.onclick = mclose;
        <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>
@@ -223,6 +228,7 @@ document.onclick = mclose;
       <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="all-permissions">
        <param name="file" value="uniref50.fa">
         <!-- <param name="debug" value="true">
                         -->
@@ -235,9 +241,9 @@ document.onclick = mclose;
        <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">
@@ -249,6 +255,7 @@ document.onclick = mclose;
       <td width="10%" valign="middle"><applet
         code="jalview.bin.JalviewLite" width="140" height="35"
         archive="jalviewApplet.jar">
+<param name="permissions" value="all-permissions">
        <param name="file" value="jpred_msa.fasta">
         <param name="jnetfile" value="jpred_msa.seq.concise">
          <param name="defaultColour" value="Clustal">
@@ -262,9 +269,9 @@ document.onclick = mclose;
        <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>
@@ -281,6 +288,7 @@ document.onclick = mclose;
       <td width="10%" valign="center"><applet
         code="jalview.bin.JalviewLite" width="140" height="35"
         archive="jalviewApplet.jar">
+<param name="permissions" value="all-permissions">
        <param name="file" value="RF00031_folded.stk">
         <param name="defaultColour" value="Purine/Pyrimidine">
          <param name="showAnnotation" value="true">
@@ -319,4 +327,4 @@ Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatic
 </div>
 </body>
 </html>
-          
\ No newline at end of file
+