X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Flinkedapplets_ng.html;h=9c8871019a8c91d10981249a1b3cdc55d86de67d;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=fbb41ec72933690de82e68f212921ea5a5da87b6;hpb=0ef644278439861e64ca6c5fe11f8fe9bc75a6a8;p=jalview.git

diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html
index fbb41ec..9c88710 100644
--- a/examples/linkedapplets_ng.html
+++ b/examples/linkedapplets_ng.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> 
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -15,38 +15,14 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
-<html xmlns="http://www.w3.org/1999/xhtml">
 <head>
-<title>Linked Jalview Applets Demo</title>
+  <TITLE>Linked JalviewLites</TITLE>
   <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /> 
   
  <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";
-  
-  function lJvApp() {
-    var jvapp = document.getElementById("jvapp");
-    var jvfollower = document.getElementById("jvfollower");
-    setConsole(document.getElementById("stdout"));
-    //jvapp.setSeparator(""+jvapp.getSeparator());
-    linkJvJmol(jvapp);
-  };
-
-  function lJvFollow() {
-    var jvapp = document.getElementById("jvapp");
-    var jvfollower = document.getElementById("jvfollower");
-    //jvfollower.setSeparator(""+jvfollower.getSeparator());
-    linkJvJmol(jvfollower);
-  };
-</script>
  
   <!--[if IE 6]>
  <link rel="stylesheet" type="text/css" href="css/ie6.css" />
@@ -103,6 +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>
 
@@ -167,17 +148,55 @@ document.onclick = mclose;
 <div id="sideNav">
 <ul>
 <li><a href="applets.html">JalviewLite Examples</a></li>
+      <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
 <li><a href="appletParameters.html">Applet Parameters</a></li>
-<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">Jalview and Jmol demo</a></li>
+      <li ><a href="embedded.html">Embedded Alignment</a></li>
+      <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
+      <li ><a href="formComplete.html">Access from Javascript</a></li>
+      <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
+      <li class="jvlite-nav-small"><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
 </ul>
 </div>
 
 <div id="content" class="content"> 
-    <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.
+
+
+<!-- boiler plate link to alternate demopage -->
+
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
+ Examples aren't working ?<br/>Try <a href="u_linkedapplets_ng.html">the unsigned applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
+</div>
+
+<!-- content template start -->
+<script src="javascript/deployJava.js"></script>
+<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
+<script src="javascript/jalview.js" language="javascript"></script>
+<script>  //deployJava.debug="true";
+  
+  function lJvApp() {
+    var jvapp = document.getElementById("jvapp");
+    var jvfollower = document.getElementById("jvfollower");
+    setConsole(document.getElementById("stdout"));
+    //jvapp.setSeparator(""+jvapp.getSeparator());
+    linkJvJmol(jvapp);
+  };
+
+  function lJvFollow() {
+    var jvapp = document.getElementById("jvapp");
+    var jvfollower = document.getElementById("jvfollower");
+    //jvfollower.setSeparator(""+jvfollower.getSeparator());
+    linkJvJmol(jvfollower);
+  };
+</script>
+    <h2>JalviewLite Linked Applets Demo</h2>
+    <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>
 	<script> 
   var attributes = {
@@ -200,15 +219,13 @@ 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?$SEQUENCE_ID$",
-    permissions : 'all-permissions',
+    linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+    permissions : 'sandbox',
     APPLICATION_URL : "http://www.jalview.org/services/launchApp"
   };
  
@@ -235,28 +252,33 @@ 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_2 : "Uniprot"
- 
+    linkLabel_1 : "EMBL-EBI Search",
+    linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
     ,
-    linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
-    permissions : 'all-permissions',
-    APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+    linkLabel_2 : "Uniprot",
+    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');
 </script>
     <p>
 <!--      <a href="javascript:linkJvJmol()">Click Me If you don't see any messages below</a>
       <br>
-       --><form name="console" id="console"><textarea name="output"
+       -->
+<form name="console" id="console">
+<textarea name="output"
         id="stdout" rows="20" cols="80">Messages  will appear here.</textarea></form>
       <br>
 </p>
-</div>
-</div>
+<!-- content template end -->
+
+
+
+</div> <!-- end content div -->
+
+</div> <!-- content -->
+</div> <!-- pagewrap -->
 <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>
