examples/u_embedded.html

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  20 <head>
  21   <TITLE>Embedded Alignment</TITLE>
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  34
  35   <!-- dd menu -->
  36   <script type="text/javascript">
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  82   <script>
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  86   </script>
  87
  88 </head>
  89
  90
  91 <body>
  92
  93
  94   <div id="header">
  95     <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
  96     <ul id="buttons">
  97       <li id="applet"><a href="applets.html" title="applet"></a></li>
  98       <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
  99     </ul>
 100   </div>
 101
 102
 103   <div id ="nav">
 104     <div id="navInner">
 105
 106       <ul id="sddm">
 107         <li><a href="http://www.jalview.org">Home</a></li>
 108         <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
 109           <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 110             <a href="http://www.jalview.org/about/documentation">Documentation</a>
 111             <a href="http://www.jalview.org/about/citation">Publications</a>
 112             <a href="http://www.jalview.org/about/credits">Credits</a>
 113           </div>
 114         </li>
 115         <li><a href="http://www.jalview.org/faq">FAQ</a></li>
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 120             <a href="http://www.jalview.org/community/links">Links</a>
 121             <a href="http://www.jalview.org/community/community-news">Community News</a>
 122           </div>
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 124         <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
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 126             <a href="http://www.jalview.org/development/release-history">Release History</a>
 127             <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
 128             <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
 129             <a href="http://www.jalview.org/development/development-news">Development News</a>
 130           </div>
 131         </li>
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 135             <a href="http://www.jalview.org/training/training-news">Training News</a>
 136           </div>
 137         </li>
 138         <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 139       </ul>
 140       <div style="clear:both"></div>
 141     </div>
 142
 143   </div>
 144 <div id="pageWrap">
 145
 146 <div id="sideNav">
 147   <ul>
 148       <li ><a href="u_applets.html">JalviewLite Examples</a></li>
 149       <li ><a href="jalviewLiteJs.html">Javascript API</a></li>
 150       <li ><a href="appletParameters.html">Applet Parameters</a></li>
 151       <li class="jvlite-nav-small"><a href="u_embedded.html">Embedded Alignment</a></li>
 152       <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
 153       <li ><a href="u_formComplete.html">Access from Javascript</a></li>
 154       <li ><a href="u_javascriptLaunch.html">Javascript Launch</a></li>
 155       <li ><a href="u_linkedapplets_ng.html">Linked JalviewLites</a></li>
 156   </ul>
 157 </div>
 158
 159 <div id="content" class="content">
 160
 161
 162 <!-- boiler plate link to alternate demopage -->
 163
 164 <div style="width: 100%">
 165 <div style="width:35%; align:left; float:right;">
 166 <div style="margin:8px; padding:8px; border: 2px solid black; align: center; float:center;">
 167  Scary Java warnings ?<br/>Try <a href="embedded.html">the signed applet demos</a>
 168 </div>
 169 <div style="margin:8px; padding:10px; align: left;">
 170 <p>Quick Links to jars for example:<br/><a href="u_jalviewApplet.jar">jalviewApplet.jar</a> and <a href="u_JmolApplet-12.2.4.jar">JmolApplet.jar</a>
 171 </p></div>
 172 </div>
 173 </div>
 174
 175 <!-- content template start -->
 176 <h2>Embedded viewing of Alignments</h2>
 177 <p>The alignment below was generated from the following files:
 178   <ul>
 179     <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
 180       FASTA format</li>
 181     <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
 182       Format Sequence Features file</li>
 183     <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
 184       Jalview Alignment Annotations File</li>
 185   </ul>
 186   <applet
 187    code="jalview.bin.JalviewLite" width="756" height="560"
 188    archive="u_jalviewApplet.jar">
 189 <param name="file" value="plantfdx.fa"/>
 190 <param name="features" value="plantfdx.features"/>
 191 <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF"/>
 192 <param name="showFullId" value="false"/>
 193 <param name="embedded" value="true"/>
 194    <param name="linkLabel_1" value="Uniprot"/>
 195    <param name="linkUrl_1"
 196      value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 197    <param name="linkLabel_2" value="EMBL-EBI Search"/>
 198    <param name="linkUrl_2"
 199      value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 200    <param name="APPLICATION_URL"
 201      value="http://www.jalview.org/services/launchApp"/>
 202 </applet>
 203 </p>
 204 <!-- content template end -->
 205
 206
 207
 208 </div> <!-- end content div -->
 209
 210 </div> <!-- content -->
 211 </div> <!-- pagewrap -->
 212 <div id ="footer">
 213 <div id="innerFooter">
 214 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
 215 <div id="cite">
 216 <p>
 217 If you use Jalview in your work, please cite this publication:
 218 </p>
 219 <br />
 220 <p>
 221 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 222 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
 223 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
 224 </p>
 225 </div>
 226 </div>
 227 </div>
 228 </body>
 229 </html>