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>Access from Javascript</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;
82 <!--//--><![CDATA[//><!--
83 var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
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="applets.html">JalviewLite Examples</a></li>
148 <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
149 <li ><a href="appletParameters.html">Applet Parameters</a></li>
150 <li ><a href="embedded.html">Embedded Alignment</a></li>
151 <li ><a href="embeddedWJmol.html">Jalview and Jmol</a></li>
152 <li class="jvlite-nav-small"><a href="formComplete.html">Access from Javascript</a></li>
153 <li ><a href="javascriptLaunch.html">Javascript Launch</a></li>
154 <li ><a href="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 Working on Snow Leopard or Java out of date ? Try <a href="u_formComplete.html">the unsigned applet demos</a>
170 <!-- content template start -->
171 <h2><a href="jalviewLiteJs.html">JalviewLite API</a> Demo</h2>
172 <p>Using the Javascript API to fill out forms using data from JalviewLite
173 <br/>Click the Javascript buttons below to interact with the Applet
174 instance on the page.</p>
175 View the source in your browser to see how it has been done. <br/>
176 <a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
177 <applet code="jalview.bin.JalviewLite" width="0" height="0"
178 archive="jalviewApplet.jar" name="Jalview">
180 <param name="file" value="plantfdx.fa"/>
181 <param name="features" value="plantfdx.features"/>
182 <param name="wrap" value="true"/>
183 <param name="showAnnotation" value="false"/>
184 <param name="windowHeight" value="500"/>
185 <param name="windowWidth" value="650"/>
186 <param name="showFullId" value="false"/>
187 <param name="linkLabel_1" value="Uniprot"/>
188 <param name="linkUrl_1"
189 value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
190 <param name="linkLabel_2" value="Expasy">
191 <param name="linkUrl_2"
192 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$"/>
193 <param name="hidefeaturegroups" value="uniprot" />
194 <param name="showbutton" value="false" />
196 <form name="exampleForm"><br/>
198 <center><strong>Using the Jalview Applet for Input
199 to an HTML Form</strong></center>
200 <div align="center"><input type="button"
201 onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
202 value="Fill Form from Jalview" /> <br/>
204 <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
206 <center><strong>Make a new View and Get and Set
207 Group Display List</strong></center>
208 <form name="groupForm">
209 <div align="center"><input type="button"
210 onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
211 value="Get groups" /> <input type="button"
212 onClick="document.applets.Jalview.newView()" value="new View" /> <br/>
213 <textarea name="groups" cols="55" rows="9"></textarea> <br/>
215 onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
216 value="Display groups" /> <input type="button"
217 onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
218 value="Hide groups" /></div>
221 <!-- content template end -->
225 </div> <!-- end content div -->
227 </div> <!-- content -->
228 </div> <!-- pagewrap -->
230 <div id="innerFooter">
231 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
234 If you use Jalview in your work, please cite this publication:
238 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
239 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
240 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>