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/>.
20 <TITLE>Linked JalviewLite applets</TITLE>
21 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
23 <link href="css/reset.css" rel="stylesheet" type="text/css" />
24 <link href="css/style.css" rel="stylesheet" type="text/css" />
27 <link rel="stylesheet" type="text/css" href="css/ie6.css" />
31 <link rel="stylesheet" type="text/css" href="css/ie7.css" />
35 <script type="text/javascript">
48 if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
50 // get new layer and show it
51 ddmenuitem = document.getElementById(id);
52 ddmenuitem.style.visibility = 'visible';
58 if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
64 closetimer = window.setTimeout(mclose, timeout);
68 function mcancelclosetime()
72 window.clearTimeout(closetimer);
77 // close layer when click-out
78 document.onclick = mclose;
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94 <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
96 <li id="applet"><a href="applets.html" title="applet"></a></li>
97 <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
106 <li><a href="http://www.jalview.org">Home</a></li>
107 <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
108 <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
109 <a href="http://www.jalview.org/about/documentation">Documentation</a>
110 <a href="http://www.jalview.org/about/citation">Publications</a>
111 <a href="http://www.jalview.org/about/credits">Credits</a>
114 <li><a href="http://www.jalview.org/faq">FAQ</a></li>
115 <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
116 <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
117 <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
118 <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
119 <a href="http://www.jalview.org/community/links">Links</a>
120 <a href="http://www.jalview.org/community/community-news">Community News</a>
123 <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
124 <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
125 <a href="http://www.jalview.org/development/release-history">Release History</a>
126 <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
127 <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
128 <a href="http://www.jalview.org/development/development-news">Development News</a>
131 <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
132 <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
133 <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
134 <a href="http://www.jalview.org/training/training-news">Training News</a>
137 <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
139 <div style="clear:both"></div>
147 <li ><a href="u_applets.html">JalviewLite Examples</a></li>
148 <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
149 <li ><a href="u_appletParameters.html">Applet Parameters</a></li>
150 <li ><a href="u_embedded.html">Embedded Alignment</a></li>
151 <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
152 <li ><a href="u_formComplete.html">Access from Javascript</a></li>
153 <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
154 <li class="jvlite-nav-small"><a href="u_linkedapplets_ng.html">Linked JalviewLite applets</a></li>
158 <div id="content" class="content">
161 <!-- boiler plate link to alternate demopage -->
163 <div style="width: 100%">
164 <div style="float:left;">
165 </div><div style="border: 2px solid black; align: left; float:right;">
166 Scary Java warnings ? Try <a href="linkedapplets_ng.html">the signed applet demos</a>
170 <!-- content template start -->
171 <script src="http://www.java.com/js/deployJava.js"></script>
172 <script src="javascript/jalview.js" language="javascript"></script>
173 <script> //deployJava.debug="true";
176 var jvapp = document.getElementById("jvapp");
177 var jvfollower = document.getElementById("jvfollower");
178 setConsole(document.getElementById("stdout"));
179 //jvapp.setSeparator(""+jvapp.getSeparator());
183 function lJvFollow() {
184 var jvapp = document.getElementById("jvapp");
185 var jvfollower = document.getElementById("jvfollower");
186 //jvfollower.setSeparator(""+jvfollower.getSeparator());
187 linkJvJmol(jvfollower);
190 <h2>JalviewLite Linked Applets Demo</h2>
191 <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.
195 code : 'jalview.bin.JalviewLite',
196 archive : 'u_jalviewApplet.jar',
199 mayscript : 'True', scriptable: 'True',
204 automaticScrolling : "true",
205 file : "plantfdx.fa",
206 annotations : "plantfdx.annotations",
210 showAnnotation : "true",
212 showFullId : "false",
214 linkLabel_1 : "EMBL-EBI Search",
215 linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
217 linkLabel_2 : "Uniprot"
219 linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
220 permissions : 'sandbox',
221 APPLICATION_URL : "http://www.jalview.org/services/launchApp"
224 deployJava.runApplet(attributes, parameters, '1.6');
228 code : 'jalview.bin.JalviewLite',
229 archive : 'u_jalviewApplet.jar',
232 mayscript : 'True', scriptable: 'True',
236 oninit : "lJvFollow",
237 file : "plantfdx.fa",
238 annotations : "plantfdx.annotations",
239 automaticScrolling : "true",
243 showAnnotation : "true",
245 showFullId : "false",
247 linkLabel_1 : "EMBL-EBI Search",
248 linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
250 linkLabel_2 : "Uniprot"
252 linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
253 permissions : 'sandbox',
254 APPLICATION_URL : "http://www.jalview.org/services/launchApp"
256 deployJava.runApplet(attributes, parameters, '1.6');
259 <!-- <a href="javascript:linkJvJmol()">Click Me If you don't see any messages below</a>
262 <form name="console" id="console">
263 <textarea name="output"
264 id="stdout" rows="20" cols="80">Messages will appear here.</textarea></form>
267 <!-- content template end -->
271 </div> <!-- end content div -->
273 </div> <!-- content -->
274 </div> <!-- pagewrap -->
276 <div id="innerFooter">
277 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
280 If you use Jalview in your work, please cite this publication:
284 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
285 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
286 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>