1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
21 <!-- InstanceBeginEditable name="doctitle" -->
22 <TITLE>JalviewLite Applet API and Form Complete Example</TITLE>
23 <!-- InstanceEndEditable -->
24 <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta http-equiv="keywords" content="jalview,multiple,sequence,alignment,editor,viewer,java,download,barton group,protein,dna,das,distributed annotation system">
25 <!-- InstanceBeginEditable name="head" -->
26 <!-- InstanceEndEditable -->
27 <style type="text/css">
30 font-family: Geneva, Arial, Helvetica, sans-serif;
34 font-family: Verdana, Arial, Helvetica, sans-serif;
36 text-decoration: none;
39 background-color:#000000; color: #F2F2FF;
44 <script language="JavaScript">
47 var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
49 {href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
52 function getEventTarget(e)
62 <body alink="#000000" vlink="#000000" link="#000000">
63 <script type="text/javascript">
64 var gaJsHost = (("https:" == document.location.protocol) ?
65 "https://ssl." : "http://www.");
66 document.write(unescape("%3Cscript src='" + gaJsHost +
67 "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
69 <script type="text/javascript">
71 var pageTracker = _gat._getTracker("UA-9060947-1");
72 pageTracker._trackPageview();
76 <table width="805" height="100" cellpadding="5">
78 <td background="../jalview.gif"> <a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>
81 <table width="805" border="0" cellpadding="5" cellspacing="5">
83 <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
86 <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
88 <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
91 <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
94 <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
97 <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
101 <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
104 <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
107 <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
110 <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
114 <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
118 <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
121 <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
124 <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
125 Mailing List</a></td>
128 <td align="left" valign="middle"><a
129 href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
130 class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
131 bug reports to the discussion list.</em></td>
135 <!--<td align="left" valign="middle"><br>
136 Please send problems<br>and
137 bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
141 <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
142 <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
145 <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
147 <strong>Using the <a href="jalviewLiteJs.html">JalviewLite API</a> to fill out forms using data from JalviewLite<br></strong>
148 Click the Javascript buttons below to interact with the Applet
149 instance on the page.<br>
150 View the source in your browser to see how it has been done. <br>
151 <a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
152 <applet code="jalview.bin.JalviewLite" width="140" height="35"
153 archive="jalviewApplet.jar" name="Jalview">
154 <param name="file" value="plantfdx.fa">
155 <param name="features" value="plantfdx.features">
156 <param name="wrap" value="true">
157 <param name="showAnnotation" value="false">
158 <param name="windowHeight" value="500">
159 <param name="windowWidth" value="650">
160 <param name="showFullId" value="false">
161 <param name="RGB" value="F2F2FF">
162 <param name="linkLabel_1" value="SRS">
163 <param name="linkUrl_1"
164 value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
165 <param name="linkLabel_2" value="Uniprot">
166 <param name="linkUrl_2"
167 value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
168 <param name="hidefeaturegroups" value="uniprot" />
169 <param name="showbutton" value="false" />
171 <form name="exampleForm"><br>
173 <center><strong>Using the Jalview Applet for Input
174 to an HTML Form</strong></center>
175 <div align="center"><input type="button"
176 onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
177 value="Fill Form from Jalview" /> <br>
179 <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
181 <center><strong>Make a new View and Get and Set
182 Group Display List</strong></center>
183 <form name="groupForm">
184 <div align="center"><input type="button"
185 onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
186 value="Get groups" /> <input type="button"
187 onClick="document.applets.Jalview.newView()" value="new View" /> <br>
188 <textarea name="groups" cols="55" rows="9"></textarea> <br>
190 onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
191 value="Display groups" /> <input type="button"
192 onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
193 value="Hide groups" /></div>
196 <!-- InstanceEndEditable --></td>
201 <!-- InstanceEnd --></html>