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>
22 <script src="javascript/deployJava.js"></script>
23 <script src="jmol/Jmol.js"></script>
24 <script src="javascript/jquery-1.4.4.min.js"></script>
25 <script src="javascript/jquery.timer.js"></script>
26 <script src="javascript/jquery.blockUI.js"></script>
27 <script src="javascript/jshashtable-2.1.js" language="javascript"></script>
28 <!-- <script src="archive-min.js" language="javascript"></script>
30 <script src="javascript/jalview.js" language="javascript"></script>
31 <script language="JavaScript">
32 // instead of this, we use a custom JmolApplet spec
33 // jmolInitialize('jmol');
34 jmolInitialize("","JmolApplet-12.2.4.jar");
37 var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
39 { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
46 function dbg(lvl,string) {
47 if (_console && lvl<=loglevel) {_console.value += string + "\n";}
49 var _lastTime=new Date();
62 var modeltofiles = new Array();
65 jvfollower = document.getElementById("jvA");
66 setConsole(document.getElementById("stdout"));
68 sep = jvfollower.getSeparator();
69 //jvapp.setSeparator(""+jvapp.getSeparator());
70 linkJvJmol(jvfollower, "jmolView", modeltofiles);
73 var _jvA=new Object();
75 code : 'jalview.bin.JalviewLite',
76 archive : 'jalviewApplet.jar',
84 java_arguments : "-Xmx256m",
85 externalstructureviewer : "true",
87 automaticScrolling : "true",
88 // <!-- defaultColour : "Strand Propensity", -->
89 file : "uniref50_mz.fa",
91 relaxedidmatch : "true",
95 showAnnotation : "false",
100 linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
102 linkLabel_2 : "Uniprot"
104 linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
105 APPLICATION_URL : "http://www.jalview.org/services/launchApp",
106 PDBfile : "1gaq.txt FER1_MAIZE"
108 jmolSetCallback("hoverCallback","_jmolhover");
109 jmolSetCallback("pickCallback","_jmolpick");
110 modeltofiles+="1gaq.txt";
112 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
114 <link href="css/reset.css" rel="stylesheet" type="text/css" />
115 <link href="css/style.css" rel="stylesheet" type="text/css" />
118 <link rel="stylesheet" type="text/css" href="css/ie6.css" />
122 <link rel="stylesheet" type="text/css" href="css/ie7.css" />
126 <script type="text/javascript">
135 // cancel close timer
139 if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
141 // get new layer and show it
142 ddmenuitem = document.getElementById(id);
143 ddmenuitem.style.visibility = 'visible';
146 // close showed layer
149 if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
153 function mclosetime()
155 closetimer = window.setTimeout(mclose, timeout);
158 // cancel close timer
159 function mcancelclosetime()
163 window.clearTimeout(closetimer);
168 // close layer when click-out
169 document.onclick = mclose;
180 <div id="logo"><a href="/" title="Home"></a></div>
182 <li id="applet"><a href="applets.html" title="applet"></a></li>
183 <li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
192 <li><a href="#">Home</a></li>
193 <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
194 <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
195 <a href="#">Documentation</a>
196 <a href="#">Publications</a>
197 <a href="#">Credits</a>
198 <a href="#">Screenshots</a>
201 <li><a href="#">FAQ</a></li>
202 <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
203 <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
204 <a href="#">News Mailing List</a>
205 <a href="#">Discussion Mailing List</a>
206 <a href="#">Links</a>
207 <a href="#">Community News</a>
210 <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
211 <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
212 <a href="#">Release History</a>
213 <a href="#">Jalview Bug Tracker</a>
214 <a href="#">Jalview Git Web</a>
215 <a href="#">Development News</a>
218 <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
219 <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
220 <a href="#">Training Courses</a>
221 <a href="#">Training News</a>
224 <li><a href="#" class="download-right">Download</a></li>
226 <div style="clear:both"></div>
236 <li><a href="applets.html">JalviewLite Examples</a></li>
237 <li><a href="appletParameters.html">Applet Parameters</a></li>
238 <li><a href="jalviewLiteJs.html">Javascript API</a></li>
239 <li><a href="formComplete.html">in-page API demo</a></li>
240 <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
241 <li class="jvlite-nav-small"><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
245 <div id="content" class="content">
248 jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
251 deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
257 <div id="innerFooter">
258 <div id="copyright"><p>Copyright all rights reserved 2012</p></div>
261 If you use Jalview in your work, please cite this publication:
265 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
266 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
267 Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033