examples/u_formComplete.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 2.8.0b1)
   4  * Copyright (C) 2014 The Jalview Authors
   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  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <head>
  21   <TITLE>Access from Javascript</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" />
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  26
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  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
  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>
 116         <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
 117           <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 118             <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
 119             <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
 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>
 123         </li>
 124         <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
 125           <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 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>
 132         <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
 133           <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 134             <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
 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 ><a href="u_embedded.html">Embedded Alignment</a></li>
 152       <li ><a href="u_embeddedWJmol.html">Jalview and Jmol</a></li>
 153       <li class="jvlite-nav-small"><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="formComplete.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><a href="jalviewLiteJs.html">JalviewLite API</a> Demo</h2>
 177 <p>Using the Javascript API to fill out forms using data from JalviewLite
 178 <br/>Click the Javascript buttons below to interact with the Applet
 179 instance on the page.</p>
 180 View the source in your browser to see how it has been done. <br/>
 181 <a name="api">View the full <a href="jalviewLiteJs.html">JalviewLite API documentation</a>.</a>
 182 <applet code="jalview.bin.JalviewLite" width="0" height="0"
 183         archive="u_jalviewApplet.jar" name="Jalview">
 184
 185   <param name="file" value="plantfdx.fa"/>
 186   <param name="features" value="plantfdx.features"/>
 187   <param name="wrap" value="true"/>
 188   <param name="showAnnotation" value="false"/>
 189   <param name="windowHeight" value="500"/>
 190   <param name="windowWidth" value="650"/>
 191   <param name="showFullId" value="false"/>
 192   <param name="linkLabel_1" value="Uniprot"/>
 193   <param name="linkUrl_1"
 194          value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 195   <param name="linkLabel_2" value="Expasy">
 196   <param name="linkUrl_2"
 197          value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$"/>
 198   <param name="hidefeaturegroups" value="uniprot" />
 199   <param name="showbutton" value="false" />
 200 </applet>
 201 <form name="exampleForm"><br/>
 202   <br/>
 203   <center><strong>Using the Jalview Applet for Input
 204       to an HTML Form</strong></center>
 205   <div align="center"><input type="button"
 206                              onClick="document.forms.exampleForm.exampleTextarea.value=document.applets.Jalview.getAlignment('fasta', 'false')"
 207                              value="Fill Form from Jalview" /> <br/>
 208     <br/>
 209     <textarea name="exampleTextarea" cols="55" rows="9"></textarea></div>
 210 </form>
 211 <center><strong>Make a new View and Get and Set
 212     Group Display List</strong></center>
 213 <form name="groupForm">
 214   <div align="center"><input type="button"
 215                              onClick="document.forms.groupForm.groups.value=document.applets.Jalview.getFeatureGroups()"
 216                              value="Get groups" /> <input type="button"
 217                                                           onClick="document.applets.Jalview.newView()" value="new View" /> <br/>
 218     <textarea name="groups" cols="55" rows="9"></textarea> <br/>
 219     <input type="button"
 220            onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, true)"
 221            value="Display groups" /> <input type="button"
 222                                             onClick="document.applets.Jalview.setFeatureGroupState(document.forms.groupForm.groups.value, false)"
 223                                             value="Hide groups" /></div>
 224 </form>
 225 </div>
 226 <!-- content template end -->
 227
 228
 229
 230 </div> <!-- end content div -->
 231
 232 </div> <!-- content -->
 233 </div> <!-- pagewrap -->
 234 <div id ="footer">
 235 <div id="innerFooter">
 236 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
 237 <div id="cite">
 238 <p>
 239 If you use Jalview in your work, please cite this publication:
 240 </p>
 241 <br />
 242 <p>
 243 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 244 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
 245 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
 246 </p>
 247 </div>
 248 </div>
 249 </div>
 250 </body>
 251 </html>