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
  83 </head>
  84
  85
  86 <body>
  87
  88
  89 <div id="header">
  90 <div id="logo"><a href="/" title="Home"></a></div>
  91 <ul id="buttons">
  92 <li id="applet"><a href="applets.html" title="applet"></a></li>
  93 <li id="desktop"><a href="/webstart/jalview.jnlp" title="desktop"></a></li>
  94 </ul>
  95 </div>
  96
  97
  98 <div id ="nav">
  99 <div id="navInner">
 100
 101 <ul id="sddm">
 102  <li><a href="#">Home</a></li>
 103  <li><a href="#" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
 104   <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 105   <a href="#">Documentation</a>
 106   <a href="#">Publications</a>
 107   <a href="#">Credits</a>
 108   <a href="#">Screenshots</a>
 109   </div>
 110  </li>
 111  <li><a href="#">FAQ</a></li>
 112  <li><a href="#" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
 113   <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 114   <a href="#">News Mailing List</a>
 115   <a href="#">Discussion Mailing List</a>
 116   <a href="#">Links</a>
 117   <a href="#">Community News</a>
 118   </div>
 119  </li>
 120  <li><a href="#" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
 121   <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 122   <a href="#">Release History</a>
 123   <a href="#">Jalview Bug Tracker</a>
 124   <a href="#">Jalview Git Web</a>
 125   <a href="#">Development News</a>
 126   </div>
 127  </li>
 128  <li><a href="#" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
 129   <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 130   <a href="#">Training Courses</a>
 131   <a href="#">Training News</a>
 132   </div>
 133  </li>
 134  <li><a href="#" class="download-right">Download</a></li>
 135 </ul>
 136 <div style="clear:both"></div>
 137 </div>
 138
 139 </div>
 140
 141
 142 <div id="pageWrap">
 143
 144 <div id="sideNav">
 145 <ul>
 146 <li><a href="applets.html">JalviewLite Examples</a></li>
 147 <li><a href="appletParameters.html">Applet Parameters</a></li>
 148 <li><a href="jalviewLiteJs.html">Javascript API</a></li>
 149 <li><a href="formComplete.html">in-page API demo</a></li>
 150 <li class="jvlite-nav-small"><a href="embedded.html">Embedded applet demo</a></li>
 151 <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
 152 <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
 153 </ul>
 154 </div>
 155
 156 <div id="content" class="content">
 157 <h1>Embedded viewing of Alignments</h1>
 158 <p>The alignment below was generated from the following files:
 159 <ul>
 160         <li><a href="plantfdx.fa">plantfdx.fa</a> - Alignment file in
 161         FASTA format</li>
 162         <li><a href="plantfdx.features">plantfdx.features</a> - Jalview
 163         Format Sequence Features file</li>
 164         <li><a href="plantfdx.annotations">plantfdx.annotations</a> -
 165         Jalview Alignment Annotations File</li>
 166 </ul>
 167 <applet code="jalview.bin.JalviewLite"
 168                         width="756" height="560" archive="jalviewApplet.jar">
 169                         <param name="file" value="plantfdx.fa">
 170                         <param name="annotations" value="plantfdx.annotations">
 171                         <param name="features" value="plantfdx.features">
 172                         <param name="embedded" value="true">
 173                         <param name="userDefinedColour"
 174                                 value="C=yellow; R,K,H=FF5555; D,E=5555FF">
 175                         <param name="showFullId" value="false">
 176        <param name="linkLabel_1" value="Uniprot">
 177         <param name="linkUrl_1"
 178          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
 179          <param name="linkLabel_2" value="Expasy">
 180           <param name="linkUrl_2"
 181            value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
 182                         <param name="APPLICATION_URL"
 183                                 value="http://www.jalview.org/services/launchApp">
 184                 </applet>
 185 </p>
 186 </body>
 187 </html>