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>JalviewLite Applet API and Form Complete Example</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></li>
149 <li class="jvlite-nav-small"><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 <strong>Using the <a href="jalviewLiteJs.html">JalviewLite API</a> to fill out forms using data from JalviewLite<br></strong>
157 Click the Javascript buttons below to interact with the Applet
158 instance on the page.<br>
159 View the source in your browser to see how it has been done. <br>
160 <a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
161 <applet code="jalview.bin.JalviewLite" width="0" height="0"
162 archive="jalviewApplet.jar" name="Jalview">
163 <param name="file" value="plantfdx.fa">
164 <param name="features" value="plantfdx.features">
165 <param name="wrap" value="true">
166 <param name="showAnnotation" value="false">
167 <param name="windowHeight" value="500">
168 <param name="windowWidth" value="650">
169 <param name="showFullId" value="false">
170 <param name="linkLabel_1" value="Uniprot">
171 <param name="linkUrl_1"
172 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
173 <param name="linkLabel_2" value="Expasy">
174 <param name="linkUrl_2"
175 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
176 <param name="hidefeaturegroups" value="uniprot" />
177 <param name="showbutton" value="false" />
179 <form name="exampleForm"><br>
181 <center><strong>Using the Jalview Applet for Input
182 to an HTML Form</strong></center>
183 <div align="center"><input type="button"
184 onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
185 value="Fill Form from Jalview" /> <br>
187 <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
189 <center><strong>Make a new View and Get and Set
190 Group Display List</strong></center>
191 <form name="groupForm">
192 <div align="center"><input type="button"
193 onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
194 value="Get groups" /> <input type="button"
195 onClick="document.applets.Jalview.newView()" value="new View" /> <br>
196 <textarea name="groups" cols="55" rows="9"></textarea> <br>
198 onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
199 value="Display groups" /> <input type="button"
200 onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
201 value="Hide groups" /></div>
206 <div id="innerFooter">
207 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
210 If you use Jalview in your work, please cite this publication:
214 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
215 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
216 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
222 <script type="text/javascript">
223 var gaJsHost = (("https:" == document.location.protocol) ?
224 "https://ssl." : "http://www.");
225 document.write(unescape("%3Cscript src=\'" + gaJsHost +
226 "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E"));
228 <script type="text/javascript">
230 var pageTracker = _gat._getTracker("'UA-9060947-1'");
231 pageTracker._trackPageview();