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>Linked Jalview Applets Demo</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" />
26 <script src="http://www.java.com/js/deployJava.js"></script>
27 <script src="javascript/jalview.js" language="javascript"></script>
28 <script> //deployJava.debug="true";
31 var jvapp = document.getElementById("jvapp");
32 var jvfollower = document.getElementById("jvfollower");
33 setConsole(document.getElementById("stdout"));
34 //jvapp.setSeparator(""+jvapp.getSeparator());
38 function lJvFollow() {
39 var jvapp = document.getElementById("jvapp");
40 var jvfollower = document.getElementById("jvfollower");
41 //jvfollower.setSeparator(""+jvfollower.getSeparator());
42 linkJvJmol(jvfollower);
47 <link rel="stylesheet" type="text/css" href="css/ie6.css" />
51 <link rel="stylesheet" type="text/css" href="css/ie7.css" />
55 <script type="text/javascript">
68 if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
70 // get new layer and show it
71 ddmenuitem = document.getElementById(id);
72 ddmenuitem.style.visibility = 'visible';
78 if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
84 closetimer = window.setTimeout(mclose, timeout);
88 function mcancelclosetime()
92 window.clearTimeout(closetimer);
97 // close layer when click-out
98 document.onclick = mclose;
109 <div id="logo"><a href="/" title="Home"></a></div>
111 <li id="applet"><a href="applets.html" title="applet"></a></li>
112 <li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
121 <li><a href="#">Home</a></li>
122 <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
123 <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
124 <a href="#">Documentation</a>
125 <a href="#">Publications</a>
126 <a href="#">Credits</a>
127 <a href="#">Screenshots</a>
130 <li><a href="#">FAQ</a></li>
131 <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
132 <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
133 <a href="#">News Mailing List</a>
134 <a href="#">Discussion Mailing List</a>
135 <a href="#">Links</a>
136 <a href="#">Community News</a>
139 <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
140 <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
141 <a href="#">Release History</a>
142 <a href="#">Jalview Bug Tracker</a>
143 <a href="#">Jalview Git Web</a>
144 <a href="#">Development News</a>
147 <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
148 <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
149 <a href="#">Training Courses</a>
150 <a href="#">Training News</a>
153 <li><a href="#" class="download-right">Download</a></li>
155 <div style="clear:both"></div>
165 <li><a href="applets.html">JalviewLite Examples</a></li>
166 <li><a href="appletParameters.html">Applet Parameters</a></li>
167 <li><a href="jalviewLiteJs.html">Javascript API</a></li>
168 <li><a href="formComplete.html">in-page API demo</a></li>
169 <li class="jvlite-nav-small"><a href="linkedApplets_ng.html">Two JalviewLites demo</a></li>
170 <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
174 <div id="content" class="content">
175 <strong>JalviewLite Linked Applets Demo<br></strong>
176 <p>The two applets below use <a href="JalviewLiteJs.html">JalviewLite's javascript API</a> to exchange events about the currently selected region and mouse position in the alignment.
180 code : 'jalview.bin.JalviewLite',
181 archive : 'jalviewApplet.jar',
184 mayscript : 'True', scriptable: 'True',
189 automaticScrolling : "true",
190 file : "plantfdx.fa",
191 annotations : "plantfdx.annotations",
195 showAnnotation : "true",
197 showFullId : "false",
200 linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
203 linkLabel_2 : "Uniprot"
206 linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
207 APPLICATION_URL : "http://www.jalview.org/services/launchApp"
210 deployJava.runApplet(attributes, parameters, '1.6');
214 code : 'jalview.bin.JalviewLite',
215 archive : 'jalviewApplet.jar',
218 mayscript : 'True', scriptable: 'True',
222 oninit : "lJvFollow",
223 file : "plantfdx.fa",
224 annotations : "plantfdx.annotations",
225 automaticScrolling : "true",
229 showAnnotation : "true",
231 showFullId : "false",
234 linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
237 linkLabel_2 : "Uniprot"
240 linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
241 APPLICATION_URL : "http://www.jalview.org/services/launchApp"
243 deployJava.runApplet(attributes, parameters, '1.6');
246 <!-- <a href="javascript:linkJvJmol()">Click Me If you don't see any messages below</a>
248 --><form name="console" id="console"><textarea name="output"
249 id="stdout" rows="20" cols="80">Messages will appear here.</textarea></form>
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>
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