examples/embedded.html

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   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
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  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
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  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();
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  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
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  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[//><!--
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  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>
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 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>