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 <head><title>Opening JalviewLite from Javascript</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;
90 <div id="logo"><a href="/" title="Home"></a></div>
92 <li id="applet"><a href="applets.html" title="applet"></a></li>
93 <li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
102 <li><a href="#">Home</a></li>
103 <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
104 <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
105 <a href="#">Documentation</a>
106 <a href="#">Publications</a>
107 <a href="#">Credits</a>
108 <a href="#">Screenshots</a>
111 <li><a href="#">FAQ</a></li>
112 <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
113 <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
114 <a href="#">News Mailing List</a>
115 <a href="#">Discussion Mailing List</a>
116 <a href="#">Links</a>
117 <a href="#">Community News</a>
120 <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
121 <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
122 <a href="#">Release History</a>
123 <a href="#">Jalview Bug Tracker</a>
124 <a href="#">Jalview Git Web</a>
125 <a href="#">Development News</a>
128 <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
129 <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
130 <a href="#">Training Courses</a>
131 <a href="#">Training News</a>
134 <li><a href="#" class="download-right">Download</a></li>
136 <div style="clear:both"></div>
146 <li><a href="applets.html">JalviewLite Examples</a></li>
147 <li><a href="appletParameters.html">Applet Parameters</a></li>
148 <li><a href="jalviewLiteJs.html">Javascript API</a><ul><li class="jvlite-nav-small"><a href="javascriptLaunch.html">JalviewLite Button</a></li></ul></li>
149 <li><a href="formComplete.html">in-page API demo</a></li>
150 <li><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
151 <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
155 <div id="content" class="content">
156 <SCRIPT type="text/javascript">
158 // From http://snipplr.com/view.php?codeview&id=1272
159 //----------------------------------------
160 //Wrapper function for constructing a request object.
162 // reqType: The HTTP request type, such as GET or POST.
163 // url: The URL of the server program.
164 // asynch: Whether to send the request asynchronously or not.
165 //----------------------------------------
167 function httpRequest(reqType,url,asynch,respHandle) {
169 // Mozilla-based browsers
170 if (window.XMLHttpRequest) {
171 request = new XMLHttpRequest();
172 } else if (window.ActiveXObject) {
173 request = new ActiveXObject("Msxml2.XMLHTTP");
175 request = new ActiveXObject("Microsoft.XMLHTTP");
179 // Request could still be null if neither ActiveXObject
180 // initialization succeeded
182 // If the reqType param is POST, then the fifth arg is the POSTed data
183 if (reqType.toLowerCase() != "post") {
184 initReq(reqType, url, asynch, respHandle);
187 var args = arguments[5];
188 if (args != null && args.length > 0) {
189 initReq(reqType, url, asynch, respHandle, args);
193 alert("Your browser does not permit the use of all " +
194 "of this application's features!");
199 //----------------------------------------
200 //Initialize a request object that is already constructed
201 //----------------------------------------
203 function initReq(reqType, url, bool, respHandle) {
205 // Specify the function that will handle the HTTP response
206 request.onreadystatechange = respHandle;
207 request.open(reqType, url, bool);
208 // If the reqType param is POST, then the
209 // fifth argument to the function is the POSTed data
210 if (reqType.toLowerCase() == "post") {
211 // Set the Content-Type header for a POST request
212 request.setRequestHeader("Content-Type", "application/x-ww-form-urlencoded; charset=UTF-8");
213 request.send(arguments[4]);
218 alert("The application cannot contact the server at the moment. " +
219 "Please try again in a few seconds.\n" +
220 "Error detail: " + errv.message);
224 // jalview launching with fetched data
226 function startJalview(aligURL,title,alwvar) {
228 httpRequest("get",aligURL,true,function() {
229 if (request.readyState == 4) {
230 alignment = request.responseText;
231 eval("var "+alwvar+" = document.JalviewLite.loadAlignment(alignment,title)");
240 <applet name="JalviewLite" code="jalview.bin.JalviewLite"
241 archive="jalviewApplet.jar" width="0" height="0">
242 <param name="debug" value="true"/>
243 <param name="showbutton" value="false"/>
247 <input type="button" name="Button1" value="Start"
248 onClick="startJalview('plantfdx.fa','Button1.alignment','alwvar')"/>
255 <div id="innerFooter">
256 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
259 If you use Jalview in your work, please cite this publication:
263 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
264 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
265 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
271 <script type="text/javascript">
272 var gaJsHost = (("https:" == document.location.protocol) ?
273 "https://ssl." : "http://www.");
274 document.write(unescape("%3Cscript src=\'" + gaJsHost +
275 "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
277 <script type="text/javascript">
279 var pageTracker = _gat._getTracker("'UA-9060947-1'");
280 pageTracker._trackPageview();