--- /dev/null
+<!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/>.
+ -->
+<head>
+ <TITLE>Jalview and Jmol</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" />
+
+ <!--[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>
+ <!--//--><![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>
+<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
+// jmolInitialize('jmol');
+jmolInitialize("","u_JmolApplet-12.2.4.jar");
+function genHref()
+{
+ var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
+ for(i=0; i<11; i++)
+ { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
+ }
+ window.location=href;
+}
+</script>
+<script>
+ var loglevel=1;
+ function dbg(lvl,string) {
+ if (_console && lvl<=loglevel) {_console.value += string + "\n";}
+ }
+ var _lastTime=new Date();
+ var _path;
+ var _datazip;
+ var _zip;
+ var alignA;
+ var alignB;
+ var featuresA;
+ var featuresB;
+ var pairs;
+ var atompairs;
+ var structdata;
+ var jmolview;
+ var jvstructassoc;
+ var modeltofiles = new Array();
+
+ function lJvA() {
+ jvfollower = document.getElementById("jvA");
+ setConsole(document.getElementById("stdout"));
+
+ sep = jvfollower.getSeparator();
+ //jvapp.setSeparator(""+jvapp.getSeparator());
+ linkJvJmol(jvfollower, "jmolView", modeltofiles);
+ };
+
+ var _jvA=new Object();
+ _jvA.attributes = {
+ code : 'jalview.bin.JalviewLite',
+ archive : 'u_jalviewApplet.jar',
+ width : '500',
+ height : '350',
+ mayscript : 'True',
+ scriptable: 'True',
+ id : 'jvA'
+ };
+ _jvA.parameters = {
+ java_arguments : "-Xmx256m",
+ externalstructureviewer : "true",
+ oninit : "lJvA",
+ automaticScrolling : "true",
+// <!-- defaultColour : "Strand Propensity", -->
+ file : "uniref50_mz.fa",
+
+ relaxedidmatch : "true",
+ debug : "true",
+ wrap : "false",
+ // separator : "^",
+ showAnnotation : "false",
+ embedded : "true",
+ showFullId : "false",
+ RGB : "F2F2FF",
+ 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://www.uniprot.org/uniprot/$SEQUENCE_ID$",
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp",
+ PDBfile : "1gaq.txt FER1_MAIZE",
+ permissions : "sandbox"
+ };
+ jmolSetCallback("hoverCallback","_jmolhover");
+ jmolSetCallback("pickCallback","_jmolpick");
+ modeltofiles+="1gaq.txt";
+</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>
+
+ </div>
+<div id="pageWrap">
+
+<div id="sideNav">
+ <ul>
+ <li ><a href="u_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="u_embedded.html">Embedded Alignment</a></li>
+ <li class="jvlite-nav-small"><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
+ <li ><a href="u_formComplete.html">Access from Javascript</a></li>
+ <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
+ <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
+ </ul>
+</div>
+
+<div id="content" class="content">
+
+
+<!-- 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;">
+ Scary Java warnings ?<br/>Try <a href="embeddedWJmol.html">the signed applet demos</a>
+</div>
+<div style="margin:8px; padding:10px; align: left;">
+<p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
+</p></div>
+</div>
+</div>
+
+<!-- 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 -->
+
+
+
+</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>
+<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>
git://source.jalview.org / jalview.git / blobdiff