1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <html xmlns="http://www.w3.org/1999/xhtml">
21 <TITLE>Embedded JalviewLite talking to externally managed Jmol</TITLE>
23 <!--//--><![CDATA[//><!--
24 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);})();
27 <script src="javascript/deployJava.js"></script>
28 <script src="jmol/Jmol.js"></script>
29 <script src="javascript/jquery-1.4.4.min.js"></script>
30 <script src="javascript/jquery.timer.js"></script>
31 <script src="javascript/jquery.blockUI.js"></script>
32 <script src="javascript/jshashtable-2.1.js" language="javascript"></script>
33 <!-- <script src="archive-min.js" language="javascript"></script>
35 <script src="javascript/jalview.js" language="javascript"></script>
36 <script language="JavaScript">
37 // instead of this, we use a custom JmolApplet spec
38 // jmolInitialize('jmol');
39 jmolInitialize("","JmolApplet-12.2.4.jar");
42 var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
44 { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
51 function dbg(lvl,string) {
52 if (_console && lvl<=loglevel) {_console.value += string + "\n";}
54 var _lastTime=new Date();
67 var modeltofiles = new Array();
70 jvfollower = document.getElementById("jvA");
71 setConsole(document.getElementById("stdout"));
73 sep = jvfollower.getSeparator();
74 //jvapp.setSeparator(""+jvapp.getSeparator());
75 linkJvJmol(jvfollower, "jmolView", modeltofiles);
78 var _jvA=new Object();
80 code : 'jalview.bin.JalviewLite',
81 archive : 'jalviewApplet.jar',
89 java_arguments : "-Xmx256m",
90 externalstructureviewer : "true",
92 automaticScrolling : "true",
93 // <!-- defaultColour : "Strand Propensity", -->
94 file : "uniref50_mz.fa",
96 relaxedidmatch : "true",
100 showAnnotation : "false",
102 showFullId : "false",
105 linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
107 linkLabel_2 : "Uniprot"
109 linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
110 APPLICATION_URL : "http://www.jalview.org/services/launchApp",
111 PDBfile : "1gaq.txt FER1_MAIZE"
113 jmolSetCallback("hoverCallback","_jmolhover");
114 jmolSetCallback("pickCallback","_jmolpick");
115 modeltofiles+="1gaq.txt";
117 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
119 <link href="css/reset.css" rel="stylesheet" type="text/css" />
120 <link href="css/style.css" rel="stylesheet" type="text/css" />
123 <link rel="stylesheet" type="text/css" href="css/ie6.css" />
127 <link rel="stylesheet" type="text/css" href="css/ie7.css" />
131 <script type="text/javascript">
140 // cancel close timer
144 if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
146 // get new layer and show it
147 ddmenuitem = document.getElementById(id);
148 ddmenuitem.style.visibility = 'visible';
151 // close showed layer
154 if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
158 function mclosetime()
160 closetimer = window.setTimeout(mclose, timeout);
163 // cancel close timer
164 function mcancelclosetime()
168 window.clearTimeout(closetimer);
173 // close layer when click-out
174 document.onclick = mclose;
185 <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
187 <li id="applet"><a href="applets.html" title="applet"></a></li>
188 <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
197 <li><a href="http://www.jalview.org">Home</a></li>
198 <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
199 <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
200 <a href="http://www.jalview.org/about/documentation">Documentation</a>
201 <a href="http://www.jalview.org/about/citation">Publications</a>
202 <a href="http://www.jalview.org/about/credits">Credits</a>
205 <li><a href="http://www.jalview.org/faq">FAQ</a></li>
206 <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
207 <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
208 <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
209 <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
210 <a href="http://www.jalview.org/community/links">Links</a>
211 <a href="http://www.jalview.org/community/community-news">Community News</a>
214 <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
215 <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
216 <a href="http://www.jalview.org/development/release-history">Release History</a>
217 <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
218 <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
219 <a href="http://www.jalview.org/development/development-news">Development News</a>
222 <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
223 <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
224 <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
225 <a href="http://www.jalview.org/training/training-news">Training News</a>
228 <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
230 <div style="clear:both"></div>
240 <li><a href="applets.html">JalviewLite Examples</a></li>
241 <li><a href="appletParameters.html">Applet Parameters</a></li>
242 <li><a href="jalviewLiteJs.html">Javascript API</a></li>
243 <li><a href="formComplete.html">in-page API demo</a></li>
244 <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
245 <li class="jvlite-nav-small"><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
249 <div id="content" class="content">
252 jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
255 deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
261 <div id="innerFooter">
262 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
265 If you use Jalview in your work, please cite this publication:
269 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
270 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
271 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>