examples/embeddedWJmol.html

   1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r
   2 <html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r
   3 <head>\r
   4 <!-- InstanceBeginEditable name="doctitle" -->\r
   5 <TITLE>Embedded JalviewLite talking to externally managed Jmol</TITLE>\r
   6 <!-- InstanceEndEditable --> \r
   7 <meta http-equiv="content-type" content="text/html; charset=UTF-8">\r
   8 <meta http-equiv="keywords" content="protein,interaction,domain,alignment,barton group,structure,interface">\r
   9 <!-- InstanceBeginEditable name="head" -->\r
  10 <script src="javascript/deployJava.js"></script>\r
  11 <script src="jmol/Jmol.js"></script>\r
  12 <script src="javascript/jquery-1.4.4.min.js"></script>\r
  13 <script src="javascript/jquery.timer.js"></script>\r
  14 <script src="javascript/jquery.blockUI.js"></script>\r
  15 <script src="javascript/jshashtable-2.1.js" language="javascript"></script>\r
  16 <!-- <script src="archive-min.js" language="javascript"></script>\r
  17 -->\r
  18 <script src="javascript/jalview.js" language="javascript"></script>\r
  19 <script language="JavaScript">\r
  20 // instead of this, we use a custom JmolApplet spec\r
  21 // jmolInitialize('jmol');\r
  22 jmolInitialize("","JmolApplet-12.1.13.jar");\r
  23 function genHref()\r
  24 {\r
  25         var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";\r
  26         for(i=0; i<11; i++)\r
  27         {       href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);       \r
  28         }\r
  29         window.location=href;\r
  30 }\r
  31 </script>\r
  32 <script>\r
  33         var loglevel=1;\r
  34         function dbg(lvl,string) {\r
  35                 if (_console && lvl<=loglevel) {_console.value += string + "\n";}\r
  36         }\r
  37         var _lastTime=new Date();\r
  38         var _path;\r
  39         var _datazip;\r
  40         var _zip;\r
  41         var alignA;\r
  42         var alignB;\r
  43         var featuresA;\r
  44         var featuresB;\r
  45         var pairs;\r
  46         var atompairs;\r
  47         var structdata;\r
  48         var jmolview;\r
  49         var jvstructassoc;\r
  50         var modeltofiles = new Array();\r
  51 \r
  52         function lJvA() {\r
  53                 jvfollower = document.getElementById("jvA");\r
  54                 setConsole(document.getElementById("stdout"));\r
  55                 \r
  56                 sep = jvfollower.getSeparator();\r
  57                 //jvapp.setSeparator(""+jvapp.getSeparator());\r
  58                 linkJvJmol(jvfollower, "jmolView", modeltofiles);\r
  59         };\r
  60 \r
  61         var _jvA=new Object();\r
  62         _jvA.attributes = {\r
  63                 code : 'jalview.bin.JalviewLite',\r
  64                 archive : 'jalviewApplet.jar',\r
  65                 width : '500',\r
  66                 height : '350',\r
  67                 mayscript : 'True',\r
  68                 scriptable: 'True',\r
  69                 id : 'jvA'\r
  70         };\r
  71         _jvA.parameters = {\r
  72                         java_arguments : "-Xmx256m",\r
  73                 externalstructureviewer : "true",\r
  74           oninit : "lJvA",\r
  75                 automaticScrolling : "true",\r
  76 //              <!-- defaultColour : "Strand Propensity", -->\r
  77                 file : "uniref50_mz.fa",\r
  78                 \r
  79                 relaxedidmatch : "true",\r
  80                 debug : "true",\r
  81                 wrap : "false",\r
  82                 // separator : "^",\r
  83                 showAnnotation : "false",\r
  84                 embedded : "true",\r
  85                 showFullId : "false",\r
  86                 RGB : "F2F2FF",\r
  87                 linkLabel_1 : "SRS",\r
  88                 linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"\r
  89                 ,\r
  90                 linkLabel_2 : "Uniprot"\r
  91                 ,\r
  92                 linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$",\r
  93                 APPLICATION_URL : "http://www.jalview.org/services/launchApp",\r
  94                 PDBfile : "1gaq.txt FER1_MAIZE"\r
  95         };\r
  96         jmolSetCallback("hoverCallback","_jmolhover");\r
  97   jmolSetCallback("pickCallback","_jmolpick");\r
  98   modeltofiles+="1gaq.txt";\r
  99 </script>\r
 100 <!-- InstanceEndEditable --> \r
 101 <style type="text/css">\r
 102 <!--\r
 103 td {\r
 104   font-family: Geneva, Arial, Helvetica, sans-serif;\r
 105   font-size: 12px;\r
 106 }\r
 107 .plain {\r
 108   font-family: Verdana, Arial, Helvetica, sans-serif;\r
 109   font-size: 14px;\r
 110   text-decoration: none;\r
 111 }\r
 112 .plain:hover{\r
 113   background-color:#000000; color: #F2F2FF;\r
 114 }\r
 115  \r
 116 -->\r
 117 </style>\r
 118 <script language="JavaScript">\r
 119 function genHref()\r
 120 {\r
 121 var s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";\r
 122 for(i=0; i<8; i++)\r
 123 {href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);  }\r
 124 window.location=href;\r
 125 }\r
 126 function getEventTarget(e)\r
 127 {\r
 128 if(!e)\r
 129 e = window.event;\r
 130 if(e.target)\r
 131 return e.target;\r
 132 return e.srcElement;\r
 133 }\r
 134 </script>\r
 135 </head>\r
 136 <body alink="#000000" vlink="#000000" link="#000000">\r
 137 <script type="text/javascript">\r
 138 var gaJsHost = (("https:" == document.location.protocol) ? \r
 139 "https://ssl." : "http://www.");\r
 140 document.write(unescape("%3Cscript src='" + gaJsHost + \r
 141 "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));\r
 142 </script>\r
 143 <script type="text/javascript">\r
 144 try{\r
 145 var pageTracker = _gat._getTracker("UA-9060947-1");\r
 146 pageTracker._trackPageview();\r
 147 } catch(err) {}\r
 148 </script>\r
 149 <div align="left"> \r
 150   <table width="805" height="100" cellpadding="5">\r
 151     <tr>\r
 152       <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>\r
 153     </tr>\r
 154   </table>\r
 155   <table width="805" border="0" cellpadding="5" cellspacing="5">\r
 156     <tr> \r
 157       <td width="183" valign="top" bgcolor="#F2F2FF" border="5"> \r
 158     \r
 159     <div align="center">\r
 160           <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">\r
 161             <tr> \r
 162               <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>\r
 163             </tr>\r
 164             <tr> \r
 165               <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>\r
 166             </tr>\r
 167             <tr> \r
 168               <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>\r
 169             </tr>\r
 170             <tr> \r
 171               <td align="left" valign="middle"><a href="applets.html" class="plain">Applet \r
 172                 Version</a></td>\r
 173             </tr>\r
 174             <tr> \r
 175               <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>\r
 176             </tr>\r
 177             <tr> \r
 178               <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>\r
 179             </tr>\r
 180             <tr> \r
 181               <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>\r
 182             </tr>\r
 183             <tr>\r
 184               <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release \r
 185                 history</a></td>\r
 186             </tr>\r
 187             <tr> \r
 188               <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source \r
 189                 Code</a></td>\r
 190             </tr>\r
 191       <tr> \r
 192               <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>\r
 193             </tr>\r
 194       <tr> \r
 195               <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>\r
 196             </tr>\r
 197             <tr> \r
 198               <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News \r
 199                 Mailing List</a></td>\r
 200             </tr>\r
 201             <tr>\r
 202               <td align="left" valign="middle"><a\r
 203             href="http://www.jalview.org/mailman/listinfo/jalview-discuss"\r
 204             class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and\r
 205             bug reports to the discussion list.</em></td>\r
 206             </tr>\r
 207             <tr></tr>\r
 208             <tr>\r
 209               <!--<td align="left" valign="middle"><br>\r
 210                 Please send problems<br>and\r
 211             bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->\r
 212             </tr>\r
 213           </table>\r
 214         </div>\r
 215         <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>\r
 216           <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a> \r
 217         </div>\r
 218         </td>\r
 219       <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->\r
 220 <!-- <a onclick="colourStructs();">Colour from jalviews</a>\r
 221  -->\r
 222  <center>\r
 223     <script>\r
 224         jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");\r
 225 </script>\r
 226   <script>\r
 227     deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');\r
 228     </script>\r
 229         </center>\r
 230         </td>\r
 231         </tr>\r
 232         </table>\r
 233 <!-- <form name="console" id="console">\r
 234   <textarea name="output" id="stdout" rows="3" cols="80"\r
 235   >Messages  will appear here.</textarea></form>\r
 236         --></div>\r
 237          <!-- InstanceEndEditable --></td>\r
 238     </tr>\r
 239   </table>\r
 240 </div>\r
 241 </body>\r
 242 <!-- InstanceEnd --></html>\r
 243