-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<!--
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* 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><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
-<head>
-<!-- InstanceBeginEditable name="doctitle" -->
-<title>Linked Jalview Applets Demo</title>
-<!-- InstanceEndEditable -->
-<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta http-equiv="keywords" content="jalview,multiple,sequence,alignment,editor,viewer,java,download,barton group,protein,dna,das,distributed annotation system">
-<!-- InstanceBeginEditable name="head" -->
-<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>
-
-<!-- InstanceEndEditable -->
-<style type="text/css">
-<!--
-td {
- font-family: Geneva, Arial, Helvetica, sans-serif;
- font-size: 12px;
-}
-.plain {
- font-family: Verdana, Arial, Helvetica, sans-serif;
- font-size: 14px;
- text-decoration: none;
-}
-.plain:hover{
- background-color:#000000; color: #F2F2FF;
-}
-
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-</style>
-<script language="JavaScript">
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-{
-if(!e)
-e = window.event;
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-return e.target;
-return e.srcElement;
-}
-</script>
-</head>
-<body alink="#000000" vlink="#000000" link="#000000">
-<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>
-<div align="left">
- <table width="805" height="100" cellpadding="5">
- <tr>
- <td background="../jalview.gif"> <a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>
- </tr>
- </table>
- <table width="805" border="0" cellpadding="5" cellspacing="5">
- <tr>
- <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
-
- <div align="center">
- <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
- <tr>
- <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
- Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
- history</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
- Code</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
- Mailing List</a></td>
- </tr>
- <tr>
- <td align="left" valign="middle"><a
- href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
- class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
- bug reports to the discussion list.</em></td>
- </tr>
- <tr></tr>
- <tr>
- <!--<td align="left" valign="middle"><br>
- Please send problems<br>and
- bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
- </tr>
- </table>
- </div>
- <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
- <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
- </div>
- </td>
- <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
- <p> </p>
- <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',
- archive : 'jalviewApplet.jar',
- width : 800,
- height : 300,
- mayscript : 'True', scriptable: 'True',
- id : 'jvapp'
- };
- var parameters = {
- oninit : "lJvApp",
- automaticScrolling : "true",
- file : "plantfdx.fa",
- annotations : "plantfdx.annotations",
- debug : "true",
- wrap : "false",
- // separator : "^",
- showAnnotation : "true",
- 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"
-
- ,
- linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
- APPLICATION_URL : "http://www.jalview.org/services/launchApp"
- };
-
- deployJava.runApplet(attributes, parameters, '1.6');
-</script>
-<script>
- var attributes = {
- code : 'jalview.bin.JalviewLite',
- archive : 'jalviewApplet.jar',
- width : 800,
- height : 300,
- mayscript : 'True', scriptable: 'True',
- id : "jvfollower"
- };
- var parameters = {
- oninit : "lJvFollow",
- file : "plantfdx.fa",
- annotations : "plantfdx.annotations",
- automaticScrolling : "true",
- debug : "true",
- wrap : "false",
- // separator : "^",
- showAnnotation : "true",
- 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"
-
- ,
- linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
- APPLICATION_URL : "http://www.jalview.org/services/launchApp"
- };
- deployJava.runApplet(attributes, parameters, '1.6');
-</script>
+
+<div id="view_decorated" name="view_decorated" style="margin:8px; padding:10px; border: 2px solid red; text-align:center; display:none;"><b>Click <a href="index.html#linkedapplets_ng"> here</a> to view decorated page</b></div>
+
+<!-- boiler plate link to alternate demopage -->
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+
+</div>
+</div>
+
+
+
+
+
+<!-- content template start -->
+
+ <h2>JalviewLite Linked Applets Demo</h2>
+ <p>The two applets below use <a href="javascript:doSubmit('jalviewLiteJs')">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
+ <a href="view-source:http://www.jalview.org/builds/develop/examples/linkedapplets_ng.html" target="_blank">View the source here to see how it has been done</a> (If the link doesn't work on your browser try going to <a href="http://www.jalview.org/builds/develop/examples/linkedapplets_ng.html">this page</a> and viewing the page source manually).</p>
+
+
+<applet
+ code="jalview.bin.JalviewLite" width="800" height="300" id="jvapp" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
+<param name="oninit" value="lJvApp"/>
+<param name="automaticScrolling" value="true"/>
+<param name="file" value="plantfdx.fa"/>
+<param name="annotations" value="plantfdx.annotations"/>
+<param name="debug" value="true"/>
+<param name="wrap" value="false"/>
+<param name="showAnnotation" value="true"/>
+<param name="embedded" value="true"/>
+<param name="showFullId" value="false"/>
+<param name="RGB" value="F2F2FF"/>
+<param name="linkLabel_1" value="EMBL-EBI Search"/>
+<param name="linkUrl_1" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+<param name="linkLabel_2" value="Uniprot"/>
+<param name="linkUrl_2" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+<param name="permissions" value="sandbox"/>
+<param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
+</applet>
+
+
+
+
+<applet
+ code="jalview.bin.JalviewLite" width="800" height="300" id="jvfollower" mayscript="True" scriptable="True" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
+<param name="oninit" value="lJvFollow"/>
+<param name="file" value="plantfdx.fa"/>
+<param name="annotations" value="plantfdx.annotations"/>
+<param name="automaticScrolling" value="true"/>
+<param name="debug" value="true"/>
+<param name="wrap" value="false"/>
+<param name="showAnnotation" value="true"/>
+<param name="embedded" value="true"/>
+<param name="showFullId" value="false"/>
+<param name="RGB" value="F2F2FF"/>
+<param name="linkLabel_1" value="EMBL-EBI Search"/>
+<param name="linkUrl_1" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
+<param name="linkLabel_2" value="Uniprot"/>
+<param name="linkUrl_2" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
+<param name="permissions" value="sandbox"/>
+<param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
+</applet>
+
+
<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>
-
-</body>
-</html>
+<!-- content template end -->
\ No newline at end of file