-<!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
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * 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/>.
--->
-<html xmlns="http://www.w3.org/1999/xhtml">
+<!-- boiler plate link to alternate demopage -->
+
<head>
-<TITLE>Embedded JalviewLite talking to externally managed Jmol</TITLE>
<script>
-<!--//--><![CDATA[//><!--
+ <!--//--><![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>
<script src="javascript/deployJava.js"></script>
<script src="jmol/Jmol.js"></script>
<script src="javascript/jquery-1.4.4.min.js"></script>
<script src="javascript/jquery.timer.js"></script>
<script src="javascript/jquery.blockUI.js"></script>
<script src="javascript/jshashtable-2.1.js" language="javascript"></script>
-<!-- <script src="archive-min.js" language="javascript"></script>
--->
+
<script src="javascript/jalview.js" language="javascript"></script>
<script language="JavaScript">
// instead of this, we use a custom JmolApplet spec
}
window.location=href;
}
-</script>
-<script>
+
var loglevel=1;
function dbg(lvl,string) {
if (_console && lvl<=loglevel) {_console.value += string + "\n";}
var _jvA=new Object();
_jvA.attributes = {
code : 'jalview.bin.JalviewLite',
- archive : 'jalviewApplet.jar',
+ archive : 'jalviewApplet.jar,JmolApplet-12.2.4.jar',
width : '500',
height : '350',
mayscript : 'True',
jmolSetCallback("hoverCallback","_jmolhover");
jmolSetCallback("pickCallback","_jmolpick");
modeltofiles+="1gaq.txt";
-</script>
-<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" />
-
- <!--[if IE 6]>
- <link rel="stylesheet" type="text/css" href="css/ie6.css" />
-<![endif]-->
-
-<!--[if IE 7]>
- <link rel="stylesheet" type="text/css" href="css/ie7.css" />
-<![endif]-->
-
-<!-- dd menu -->
-<script type="text/javascript">
-<!--
-var timeout = 500;
-var closetimer = 0;
-var ddmenuitem = 0;
-
-// open hidden layer
-function mopen(id)
-{
- // cancel close timer
- mcancelclosetime();
-
- // close old layer
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
-
- // get new layer and show it
- ddmenuitem = document.getElementById(id);
- ddmenuitem.style.visibility = 'visible';
-
-}
-// close showed layer
-function mclose()
-{
- if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
-}
-
-// go close timer
-function mclosetime()
-{
- closetimer = window.setTimeout(mclose, timeout);
-}
-
-// cancel close timer
-function mcancelclosetime()
-{
- if(closetimer)
- {
- window.clearTimeout(closetimer);
- closetimer = null;
- }
-}
-
-// close layer when click-out
-document.onclick = mclose;
-// -->
-</script>
-
+</script>
</head>
-
-<body>
-
-
-<div id="header">
-<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>
-</ul>
-</div>
-
-
-<div id ="nav">
-<div id="navInner">
-
-<ul id="sddm">
- <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="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="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="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="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
- <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <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="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
- <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
- <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="http://www.jalview.org/download" class="download-right">Download</a></li>
-</ul>
-<div style="clear:both"></div>
+<div style="width: 100%">
+<div style="width:35%; align:left; float:right;">
+<div style="margin:8px; padding:10px; border: 2px solid black; 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>
-
-
-<div id="pageWrap">
-
-<div id="sideNav">
-<ul>
-<li><a href="applets.html">JalviewLite Examples</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><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
-<li class="jvlite-nav-small"><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
-</ul>
</div>
-<div id="content" class="content">
- <center>
- <script>
- jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
-</script>
- <script>
- deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
- </script>
- </center>
-</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>
+<!-- content template start -->
+<h2>Structure and Alignment</h2>
+<p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
+<center>
+ <script>
+ jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
+ </script>
+ <script>
+ deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
+ </script>
+</center>
+<!-- content template end -->
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff