examples/javascriptLaunch.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>
  21   <head><title>Opening JalviewLite 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" />
  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 <!--//--><![CDATA[//><!--
  83 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);})();
  84 //--><!]]>
  85 </head>
  86
  87
  88 <body>
  89
  90
  91 <div id="header">
  92 <div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
  93 <ul id="buttons">
  94 <li id="applet"><a href="applets.html" title="applet"></a></li>
  95 <li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
  96 </ul>
  97 </div>
  98
  99
 100 <div id ="nav">
 101 <div id="navInner">
 102
 103 <ul id="sddm">
 104  <li><a href="http://www.jalview.org">Home</a></li>
 105  <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
 106   <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 107   <a href="http://www.jalview.org/about/documentation">Documentation</a>
 108   <a href="http://www.jalview.org/about/citation">Publications</a>
 109   <a href="http://www.jalview.org/about/credits">Credits</a>
 110   </div>
 111  </li>
 112  <li><a href="http://www.jalview.org/faq">FAQ</a></li>
 113  <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
 114   <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 115   <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
 116   <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
 117   <a href="http://www.jalview.org/community/links">Links</a>
 118   <a href="http://www.jalview.org/community/community-news">Community News</a>
 119   </div>
 120  </li>
 121  <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
 122   <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 123   <a href="http://www.jalview.org/development/release-history">Release History</a>
 124   <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
 125   <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
 126   <a href="http://www.jalview.org/development/development-news">Development News</a>
 127   </div>
 128  </li>
 129  <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
 130   <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
 131   <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
 132   <a href="http://www.jalview.org/training/training-news">Training News</a>
 133   </div>
 134  </li>
 135  <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
 136 </ul>
 137 <div style="clear:both"></div>
 138 </div>
 139
 140 </div>
 141
 142
 143 <div id="pageWrap">
 144
 145 <div id="sideNav">
 146 <ul>
 147 <li><a href="applets.html">JalviewLite Examples</a></li>
 148 <li><a href="appletParameters.html">Applet Parameters</a></li>
 149 <li><a href="jalviewLiteJs.html">Javascript API</a><ul><li class="jvlite-nav-small"><a href="javascriptLaunch.html">JalviewLite Button</a></li></ul></li>
 150 <li><a href="formComplete.html">in-page API 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   <SCRIPT type="text/javascript">
 158   /* <![CDATA[ // */
 159 // From http://snipplr.com/view.php?codeview&id=1272
 160 //----------------------------------------
 161 //Wrapper function for constructing a request object.
 162 //      Parameters:
 163 //              reqType: The HTTP request type, such as GET or POST.
 164 //              url: The URL of the server program.
 165 //              asynch: Whether to send the request asynchronously or not.
 166 //----------------------------------------
 167
 168 function httpRequest(reqType,url,asynch,respHandle) {
 169
 170         // Mozilla-based browsers
 171         if (window.XMLHttpRequest) {
 172                 request = new XMLHttpRequest();
 173         } else if (window.ActiveXObject) {
 174                 request = new ActiveXObject("Msxml2.XMLHTTP");
 175                 if (!request) {
 176                         request = new ActiveXObject("Microsoft.XMLHTTP");
 177                 }
 178         }
 179
 180         // Request could still be null if neither ActiveXObject
 181         //   initialization succeeded
 182         if (request) {
 183                 // If the reqType param is POST, then the fifth arg is the POSTed data
 184                 if (reqType.toLowerCase() != "post") {
 185                         initReq(reqType, url, asynch, respHandle);
 186                 } else {
 187                         // The POSTed data
 188                         var args = arguments[5];
 189                         if (args != null && args.length > 0) {
 190                                 initReq(reqType, url, asynch, respHandle, args);
 191                         }
 192                 }
 193         } else {
 194                 alert("Your browser does not permit the use of all " +
 195                         "of this application's features!");
 196         }
 197
 198 }
 199
 200 //----------------------------------------
 201 //Initialize a request object that is already constructed
 202 //----------------------------------------
 203
 204 function initReq(reqType, url, bool, respHandle) {
 205         try {
 206                 // Specify the function that will handle the HTTP response
 207                 request.onreadystatechange = respHandle;
 208                 request.open(reqType, url, bool);
 209                 // If the reqType param is POST, then the
 210                 //   fifth argument to the function is the POSTed data
 211                 if (reqType.toLowerCase() == "post") {
 212                         // Set the Content-Type header for a POST request
 213                         request.setRequestHeader("Content-Type", "application/x-ww-form-urlencoded; charset=UTF-8");
 214                         request.send(arguments[4]);
 215                 } else {
 216                         request.send(null);
 217                 }
 218         } catch (errv) {
 219                 alert("The application cannot contact the server at the moment. " +
 220                         "Please try again in a few seconds.\n" +
 221                         "Error detail: " + errv.message);
 222         }
 223 }
 224
 225 // jalview launching with fetched data
 226
 227 function startJalview(aligURL,title,alwvar) {
 228                 var aligment = "";
 229                 httpRequest("get",aligURL,true,function() {
 230                                 if (request.readyState == 4) {
 231                                         alignment = request.responseText;
 232                                         eval("var "+alwvar+" = document.JalviewLite.loadAlignment(alignment,title)");
 233                                 }
 234                 })
 235
 236 }
 237
 238 /* ]]> */
 239 </SCRIPT>
 240   <form name="Form1">
 241 <applet name="JalviewLite"  code="jalview.bin.JalviewLite"
 242 archive="jalviewApplet.jar" width="0" height="0">
 243 <param name="debug" value="true"/>
 244 <param name="showbutton" value="false"/>
 245 <param name="permissions" value="sandbox"/>
 246 </applet>
 247
 248
 249   <input type="button" name="Button1" value="Start"
 250 onClick="startJalview('plantfdx.fa','Button1.alignment','alwvar')"/>
 251   </form>
 252
 253
 254 </div>
 255 </div>
 256 <div id ="footer">
 257 <div id="innerFooter">
 258 <div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
 259 <div id="cite">
 260 <p>
 261 If you use Jalview in your work, please cite this publication:
 262 </p>
 263 <br />
 264 <p>
 265 Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
 266 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
 267 Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
 268 </p>
 269 </div>
 270 </div>
 271 </div>
 272 </body>
 273 </head>
 274 </html>