JAL-1312 more helpful error message when translation breaks
[jalview.git] / examples / embedded.html
1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> 
2 <!--
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
5  * 
6  * This file is part of Jalview.
7  * 
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.
11  *  
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.
16  * 
17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
18 -->
19 <html xmlns="http://www.w3.org/1999/xhtml">
20 <head>Embedded viewing of Alignments
21 </title>
22 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /> 
23
24  <link href="css/reset.css" rel="stylesheet" type="text/css" />
25  <link href="css/style.css" rel="stylesheet" type="text/css" />
26  
27   <!--[if IE 6]>
28  <link rel="stylesheet" type="text/css" href="css/ie6.css" />
29 <![endif]-->
30
31 <!--[if IE 7]>
32  <link rel="stylesheet" type="text/css" href="css/ie7.css" />
33 <![endif]-->
34
35 <!-- dd menu -->
36 <script type="text/javascript">
37 <!--
38 var timeout         = 500;
39 var closetimer  = 0;
40 var ddmenuitem      = 0;
41
42 // open hidden layer
43 function mopen(id)
44
45  // cancel close timer
46  mcancelclosetime();
47
48  // close old layer
49  if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
50
51  // get new layer and show it
52  ddmenuitem = document.getElementById(id);
53  ddmenuitem.style.visibility = 'visible';
54
55 }
56 // close showed layer
57 function mclose()
58 {
59  if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
60 }
61
62 // go close timer
63 function mclosetime()
64 {
65  closetimer = window.setTimeout(mclose, timeout);
66 }
67
68 // cancel close timer
69 function mcancelclosetime()
70 {
71  if(closetimer)
72  {
73   window.clearTimeout(closetimer);
74   closetimer = null;
75  }
76 }
77
78 // close layer when click-out
79 document.onclick = mclose; 
80 // -->
81 </script>
82 <script>
83 <!--//--><![CDATA[//><!--
84 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);})();
85 //--><!]]>
86 </script>
87 </head>
88
89
90 <body>
91
92
93 <div id="header">
94 <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
95 <ul id="buttons">
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>
98 </ul>
99 </div>
100
101
102 <div id ="nav">
103 <div id="navInner">
104
105 <ul id="sddm">
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>
112   </div>
113  </li>
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>
121   </div>
122  </li>
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>
129   </div>
130  </li>
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>
135   </div>
136  </li>
137  <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
138 </ul>
139 <div style="clear:both"></div>
140 </div>
141
142 </div>
143
144
145 <div id="pageWrap">
146
147 <div id="sideNav">
148 <ul>
149 <li><a href="applets.html">JalviewLite Examples</a></li>
150 <li><a href="appletParameters.html">Applet Parameters</a></li>
151 <li><a href="jalviewLiteJs.html">Javascript API</a></li>
152 <li><a href="formComplete.html">in-page API demo</a></li>
153 <li class="jvlite-nav-small"><a href="embedded.html">Embedded applet demo</a></li>
154 <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
155 <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
156 </ul>
157 </div>
158
159 <div id="content" class="content">
160 <h1>Embedded viewing of Alignments</h1>
161 <p>The alignment below was generated from the following files:
162 <ul>
163         <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
164         FASTA format</li>
165         <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
166         Format Sequence Features file</li>
167         <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
168         Jalview Alignment Annotations File</li>
169 </ul>
170 <applet code="jalview.bin.JalviewLite"
171                         width="756" height="560" archive="jalviewApplet.jar">
172                         <param name="file" value="plantfdx.fa">
173                         <param name="annotations" value="plantfdx.annotations">
174                         <param name="features" value="plantfdx.features">
175                         <param name="embedded" value="true">
176                         <param name="userDefinedColour"
177                                 value="C=yellow; R,K,H=FF5555; D,E=5555FF">
178                         <param name="showFullId" value="false">
179        <param name="linkLabel_1" value="Uniprot">
180         <param name="linkUrl_1"
181          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
182          <param name="linkLabel_2" value="Expasy">
183           <param name="linkUrl_2"
184            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
185                         <param name="APPLICATION_URL"
186                                 value="http://www.jalview.org/services/launchApp">
187                 </applet>
188 </p>
189 </div>
190 </div>
191 <div id ="footer">
192 <div id="innerFooter">
193 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
194 <div id="cite">
195 <p>
196 If you use Jalview in your work, please cite this publication:
197 </p>
198 <br />
199 <p>
200 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
201 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
202 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
203 </p>
204 </div>
205 </div>
206 </div>
207 </body>
208 </html>