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">
20 <head>Embedded viewing of Alignments
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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>
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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></li>
149 <li><a href="formComplete.html">in-page API demo</a></li>
150 <li class="jvlite-nav-small"><a href="embedded.html">Embedded applet demo</a></li>
151 <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
152 <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
156 <div id="content" class="content">
157 <h1>Embedded viewing of Alignments</h1>
158 <p>The alignment below was generated from the following files:
160 <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
162 <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
163 Format Sequence Features file</li>
164 <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
165 Jalview Alignment Annotations File</li>
167 <applet code="jalview.bin.JalviewLite"
168 width="756" height="560" archive="jalviewApplet.jar">
169 <param name="file" value="plantfdx.fa">
170 <param name="annotations" value="plantfdx.annotations">
171 <param name="features" value="plantfdx.features">
172 <param name="embedded" value="true">
173 <param name="userDefinedColour"
174 value="C=yellow; R,K,H=FF5555; D,E=5555FF">
175 <param name="showFullId" value="false">
176 <param name="linkLabel_1" value="Uniprot">
177 <param name="linkUrl_1"
178 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
179 <param name="linkLabel_2" value="Expasy">
180 <param name="linkUrl_2"
181 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
182 <param name="APPLICATION_URL"
183 value="http://www.jalview.org/services/launchApp">
189 <div id="innerFooter">
190 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
193 If you use Jalview in your work, please cite this publication:
197 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
198 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
199 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>