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 ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 <TITLE>Jalview and Jmol</TITLE>
22 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
24 <link href="css/reset.css" rel="stylesheet" type="text/css" />
25 <link href="css/style.css" rel="stylesheet" type="text/css" />
28 <link rel="stylesheet" type="text/css" href="css/ie6.css" />
32 <link rel="stylesheet" type="text/css" href="css/ie7.css" />
36 <script type="text/javascript">
49 if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
51 // get new layer and show it
52 ddmenuitem = document.getElementById(id);
53 ddmenuitem.style.visibility = 'visible';
59 if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
65 closetimer = window.setTimeout(mclose, timeout);
69 function mcancelclosetime()
73 window.clearTimeout(closetimer);
78 // close layer when click-out
79 document.onclick = mclose;
83 <!--//--><![CDATA[//><!--
84 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);})();
87 <script src="javascript/deployJava.js"></script>
88 <script src="jmol/Jmol2.js"></script>
89 <script src="javascript/jquery-1.4.4.min.js"></script>
90 <script src="javascript/jquery.timer.js"></script>
91 <script src="javascript/jquery.blockUI.js"></script>
92 <script src="javascript/jshashtable-2.1.js" language="javascript"></script>
93 <!-- <script src="archive-min.js" language="javascript"></script>
95 <script src="javascript/jalview.js" language="javascript"></script>
96 <script language="JavaScript">
97 // instead of this, we use a custom JmolApplet spec
98 // jmolInitialize('jmol');
99 jmolInitialize("","JmolApplet-14.2.14_2015.06.11.jar");
103 function dbg(lvl,string) {
104 if (_console && lvl<=loglevel) {_console.value += string + "\n";}
106 var _lastTime=new Date();
119 var modeltofiles = new Array();
122 jvfollower = document.getElementById("jvA");
123 setConsole(document.getElementById("stdout"));
125 // sep = jvfollower.getSeparator();
126 //jvapp.setSeparator(""+jvapp.getSeparator());
127 linkJvJmol(jvfollower, "jmolView", modeltofiles);
130 var _jvA=new Object();
132 code : 'jalview.bin.JalviewLite',
133 archive : 'jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar',
141 java_arguments : "-Xmx256m",
142 externalstructureviewer : "true",
144 automaticScrolling : "true",
145 // <!-- defaultColour : "Strand Propensity", -->
146 file : "uniref50_mz.fa",
148 relaxedidmatch : "true",
152 showAnnotation : "false",
154 showFullId : "false",
156 linkLabel_1 : "EMBL-EBI Search",
157 linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
159 linkLabel_2 : "Uniprot"
161 linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
162 APPLICATION_URL : "http://www.jalview.org/services/launchApp",
163 PDBfile : "1gaq.txt FER1_MAIZE",
164 permissions : "sandbox"
166 jmolSetCallback("hoverCallback","_jmolhover");
167 jmolSetCallback("pickCallback","_jmolpick");
168 modeltofiles+="1gaq.txt";
178 <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
180 <li id="applet"><a href="applets.html" title="applet"></a></li>
181 <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
190 <li><a href="http://www.jalview.org">Home</a></li>
191 <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
192 <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
193 <a href="http://www.jalview.org/about/documentation">Documentation</a>
194 <a href="http://www.jalview.org/about/citation">Publications</a>
195 <a href="http://www.jalview.org/about/credits">Credits</a>
198 <li><a href="http://www.jalview.org/faq">FAQ</a></li>
199 <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
200 <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
201 <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
202 <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
203 <a href="http://www.jalview.org/community/links">Links</a>
204 <a href="http://www.jalview.org/community/community-news">Community News</a>
207 <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
208 <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
209 <a href="http://www.jalview.org/development/release-history">Release History</a>
210 <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
211 <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
212 <a href="http://www.jalview.org/development/development-news">Development News</a>
215 <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
216 <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
217 <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
218 <a href="http://www.jalview.org/training/training-news">Training News</a>
221 <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
223 <div style="clear:both"></div>
231 <li ><a href="applets.html">JalviewLite Examples</a></li>
232 <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
233 <li ><a href="appletParameters.html">Applet Parameters</a></li>
234 <li ><a href="embedded.html">Embedded Alignment</a></li>
235 <li class="jvlite-nav-small"><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
236 <li ><a href="formComplete.html">Access from Javascript</a></li>
237 <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
238 <li ><a href="linkedapplets_ng.html">Linked JalviewLites</a></li>
242 <div id="content" class="content">
245 <!-- boiler plate link to alternate demopage -->
247 <div style="width: 100%">
248 <div style="width:35%; align:left; float:right;">
249 <div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
250 Examples aren't working ?<br/>Try <a href="u_embeddedWJmol.html">the unsigned applet demos</a>
252 <div style="margin:8px; padding:10px; align: left;">
253 <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>
258 <!-- content template start -->
259 <h2>Structure and Alignment</h2>
260 <p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
263 jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
266 deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
269 <!-- content template end -->
273 </div> <!-- end content div -->
275 </div> <!-- content -->
276 </div> <!-- pagewrap -->
278 <div id="innerFooter">
279 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
282 If you use Jalview in your work, please cite this publication:
286 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
287 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
288 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>