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>Embedded JalviewLite talking to externally managed Jmol</TITLE>
23 <!-- InstanceEndEditable -->
24 <meta http-equiv="content-type" content="text/html; charset=UTF-8">
25 <meta http-equiv="keywords" content="protein,interaction,domain,alignment,barton group,structure,interface">
26 <!-- InstanceBeginEditable name="head" -->
27 <script src="javascript/deployJava.js"></script>
28 <script src="jmol/Jmol.js"></script>
29 <script src="javascript/jquery-1.4.4.min.js"></script>
30 <script src="javascript/jquery.timer.js"></script>
31 <script src="javascript/jquery.blockUI.js"></script>
32 <script src="javascript/jshashtable-2.1.js" language="javascript"></script>
33 <!-- <script src="archive-min.js" language="javascript"></script>
35 <script src="javascript/jalview.js" language="javascript"></script>
36 <script language="JavaScript">
37 // instead of this, we use a custom JmolApplet spec
38 // jmolInitialize('jmol');
39 jmolInitialize("","JmolApplet-12.2.4.jar");
42 var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
44 { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
51 function dbg(lvl,string) {
52 if (_console && lvl<=loglevel) {_console.value += string + "\n";}
54 var _lastTime=new Date();
67 var modeltofiles = new Array();
70 jvfollower = document.getElementById("jvA");
71 setConsole(document.getElementById("stdout"));
73 sep = jvfollower.getSeparator();
74 //jvapp.setSeparator(""+jvapp.getSeparator());
75 linkJvJmol(jvfollower, "jmolView", modeltofiles);
78 var _jvA=new Object();
80 code : 'jalview.bin.JalviewLite',
81 archive : 'jalviewApplet.jar',
89 java_arguments : "-Xmx256m",
90 externalstructureviewer : "true",
92 automaticScrolling : "true",
93 // <!-- defaultColour : "Strand Propensity", -->
94 file : "uniref50_mz.fa",
96 relaxedidmatch : "true",
100 showAnnotation : "false",
102 showFullId : "false",
105 linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
107 linkLabel_2 : "Uniprot"
109 linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
110 APPLICATION_URL : "http://www.jalview.org/services/launchApp",
111 PDBfile : "1gaq.txt FER1_MAIZE"
113 jmolSetCallback("hoverCallback","_jmolhover");
114 jmolSetCallback("pickCallback","_jmolpick");
115 modeltofiles+="1gaq.txt";
117 <!-- InstanceEndEditable -->
118 <style type="text/css">
121 font-family: Geneva, Arial, Helvetica, sans-serif;
125 font-family: Verdana, Arial, Helvetica, sans-serif;
127 text-decoration: none;
130 background-color:#000000; color: #F2F2FF;
135 <script language="JavaScript">
138 var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
140 {href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }
141 window.location=href;
143 function getEventTarget(e)
153 <body alink="#000000" vlink="#000000" link="#000000">
154 <script type="text/javascript">
155 var gaJsHost = (("https:" == document.location.protocol) ?
156 "https://ssl." : "http://www.");
157 document.write(unescape("%3Cscript src='" + gaJsHost +
158 "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
160 <script type="text/javascript">
162 var pageTracker = _gat._getTracker("UA-9060947-1");
163 pageTracker._trackPageview();
167 <table width="805" height="100" cellpadding="5">
169 <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>
172 <table width="805" border="0" cellpadding="5" cellspacing="5">
174 <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
177 <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
179 <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
182 <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
185 <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
188 <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
192 <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
195 <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
198 <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
201 <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
205 <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
209 <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
212 <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
215 <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
216 Mailing List</a></td>
219 <td align="left" valign="middle"><a
220 href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
221 class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
222 bug reports to the discussion list.</em></td>
226 <!--<td align="left" valign="middle"><br>
227 Please send problems<br>and
228 bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
232 <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
233 <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
236 <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
237 <!-- <a onclick="colourStructs();">Colour from jalviews</a>
241 jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
244 deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
250 <!-- <form name="console" id="console">
251 <textarea name="output" id="stdout" rows="3" cols="80"
252 >Messages will appear here.</textarea></form>
254 <!-- InstanceEndEditable --></td>
259 <!-- InstanceEnd --></html>