examples/embeddedWJmol.html

   1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
   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><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->
  20 <head>
  21 <!-- InstanceBeginEditable name="doctitle" -->
  22 <TITLE>Embedded JalviewLite talking to externally managed Jmol</TITLE>
  23 <!-- InstanceEndEditable -->
  24 <meta http-equiv="content-type" content="text/html; charset=UTF-8">
  25 <meta http-equiv="keywords" content="protein,interaction,domain,alignment,barton group,structure,interface">
  26 <!-- InstanceBeginEditable name="head" -->
  27 <script src="javascript/deployJava.js"></script>
  28 <script src="jmol/Jmol.js"></script>
  29 <script src="javascript/jquery-1.4.4.min.js"></script>
  30 <script src="javascript/jquery.timer.js"></script>
  31 <script src="javascript/jquery.blockUI.js"></script>
  32 <script src="javascript/jshashtable-2.1.js" language="javascript"></script>
  33 <!-- <script src="archive-min.js" language="javascript"></script>
  34 -->
  35 <script src="javascript/jalview.js" language="javascript"></script>
  36 <script language="JavaScript">
  37 // instead of this, we use a custom JmolApplet spec
  38 // jmolInitialize('jmol');
  39 jmolInitialize("","JmolApplet-12.2.4.jar");
  40 function genHref()
  41 {
  42         var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
  43         for(i=0; i<11; i++)
  44         {       href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
  45         }
  46         window.location=href;
  47 }
  48 </script>
  49 <script>
  50         var loglevel=1;
  51         function dbg(lvl,string) {
  52                 if (_console && lvl<=loglevel) {_console.value += string + "\n";}
  53         }
  54         var _lastTime=new Date();
  55         var _path;
  56         var _datazip;
  57         var _zip;
  58         var alignA;
  59         var alignB;
  60         var featuresA;
  61         var featuresB;
  62         var pairs;
  63         var atompairs;
  64         var structdata;
  65         var jmolview;
  66         var jvstructassoc;
  67         var modeltofiles = new Array();
  68
  69         function lJvA() {
  70                 jvfollower = document.getElementById("jvA");
  71                 setConsole(document.getElementById("stdout"));
  72
  73                 sep = jvfollower.getSeparator();
  74                 //jvapp.setSeparator(""+jvapp.getSeparator());
  75                 linkJvJmol(jvfollower, "jmolView", modeltofiles);
  76         };
  77
  78         var _jvA=new Object();
  79         _jvA.attributes = {
  80                 code : 'jalview.bin.JalviewLite',
  81                 archive : 'jalviewApplet.jar',
  82                 width : '500',
  83                 height : '350',
  84                 mayscript : 'True',
  85                 scriptable: 'True',
  86                 id : 'jvA'
  87         };
  88         _jvA.parameters = {
  89                         java_arguments : "-Xmx256m",
  90                 externalstructureviewer : "true",
  91           oninit : "lJvA",
  92                 automaticScrolling : "true",
  93 //              <!-- defaultColour : "Strand Propensity", -->
  94                 file : "uniref50_mz.fa",
  95
  96                 relaxedidmatch : "true",
  97                 debug : "true",
  98                 wrap : "false",
  99                 // separator : "^",
 100                 showAnnotation : "false",
 101                 embedded : "true",
 102                 showFullId : "false",
 103                 RGB : "F2F2FF",
 104                 linkLabel_1 : "SRS",
 105                 linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"
 106                 ,
 107                 linkLabel_2 : "Uniprot"
 108                 ,
 109                 linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",
 110                 APPLICATION_URL : "http://www.jalview.org/services/launchApp",
 111                 PDBfile : "1gaq.txt FER1_MAIZE"
 112         };
 113         jmolSetCallback("hoverCallback","_jmolhover");
 114   jmolSetCallback("pickCallback","_jmolpick");
 115   modeltofiles+="1gaq.txt";
 116 </script>
 117 <!-- InstanceEndEditable -->
 118 <style type="text/css">
 119 <!--
 120 td {
 121   font-family: Geneva, Arial, Helvetica, sans-serif;
 122   font-size: 12px;
 123 }
 124 .plain {
 125   font-family: Verdana, Arial, Helvetica, sans-serif;
 126   font-size: 14px;
 127   text-decoration: none;
 128 }
 129 .plain:hover{
 130   background-color:#000000; color: #F2F2FF;
 131 }
 132
 133 -->
 134 </style>
 135 <script language="JavaScript">
 136 function genHref()
 137 {
 138 var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";
 139 for(i=0; i<8; i++)
 140 {href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);  }
 141 window.location=href;
 142 }
 143 function getEventTarget(e)
 144 {
 145 if(!e)
 146 e = window.event;
 147 if(e.target)
 148 return e.target;
 149 return e.srcElement;
 150 }
 151 </script>
 152 </head>
 153 <body alink="#000000" vlink="#000000" link="#000000">
 154 <script type="text/javascript">
 155 var gaJsHost = (("https:" == document.location.protocol) ?
 156 "https://ssl." : "http://www.");
 157 document.write(unescape("%3Cscript src='" + gaJsHost +
 158 "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
 159 </script>
 160 <script type="text/javascript">
 161 try{
 162 var pageTracker = _gat._getTracker("UA-9060947-1");
 163 pageTracker._trackPageview();
 164 } catch(err) {}
 165 </script>
 166 <div align="left">
 167   <table width="805" height="100" cellpadding="5">
 168     <tr>
 169       <td background="../jalview.gif">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>
 170     </tr>
 171   </table>
 172   <table width="805" border="0" cellpadding="5" cellspacing="5">
 173     <tr>
 174       <td width="183" valign="top" bgcolor="#F2F2FF" border="5">
 175
 176     <div align="center">
 177           <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">
 178             <tr>
 179               <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>
 180             </tr>
 181             <tr>
 182               <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>
 183             </tr>
 184             <tr>
 185               <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>
 186             </tr>
 187             <tr>
 188               <td align="left" valign="middle"><a href="applets.html" class="plain">Applet
 189                 Version</a></td>
 190             </tr>
 191             <tr>
 192               <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>
 193             </tr>
 194             <tr>
 195               <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>
 196             </tr>
 197             <tr>
 198               <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>
 199             </tr>
 200             <tr>
 201               <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release
 202                 history</a></td>
 203             </tr>
 204             <tr>
 205               <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source
 206                 Code</a></td>
 207             </tr>
 208       <tr>
 209               <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>
 210             </tr>
 211       <tr>
 212               <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>
 213             </tr>
 214             <tr>
 215               <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News
 216                 Mailing List</a></td>
 217             </tr>
 218             <tr>
 219               <td align="left" valign="middle"><a
 220             href="http://www.jalview.org/mailman/listinfo/jalview-discuss"
 221             class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and
 222             bug reports to the discussion list.</em></td>
 223             </tr>
 224             <tr></tr>
 225             <tr>
 226               <!--<td align="left" valign="middle"><br>
 227                 Please send problems<br>and
 228             bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->
 229             </tr>
 230           </table>
 231         </div>
 232         <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>
 233           <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a>
 234         </div>
 235         </td>
 236       <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
 237 <!-- <a onclick="colourStructs();">Colour from jalviews</a>
 238  -->
 239  <center>
 240     <script>
 241         jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
 242 </script>
 243   <script>
 244     deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
 245     </script>
 246         </center>
 247         </td>
 248         </tr>
 249         </table>
 250 <!-- <form name="console" id="console">
 251   <textarea name="output" id="stdout" rows="3" cols="80"
 252   >Messages  will appear here.</textarea></form>
 253         --></div>
 254          <!-- InstanceEndEditable --></td>
 255     </tr>
 256   </table>
 257 </div>
 258 </body>
 259 <!-- InstanceEnd --></html>
 260