examples/embeddedWJmol.html

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 100 //--><!]]>
 101 </script>
 102 <!--[if lt IE 9]><script src="http://html5shiv.googlecode.com/svn/trunk/html5.js"></script><![endif]-->
 103
 104
 105 <script src="javascript/deployJava.js"></script>
 106 <script src="jmol/Jmol2.js"></script>
 107 <script src="javascript/jquery-1.4.4.min.js"></script>
 108 <script src="javascript/jquery.timer.js"></script>
 109 <script src="javascript/jquery.blockUI.js"></script>
 110 <script src="javascript/jshashtable-2.1.js" language="javascript"></script>
 111 <script src="javascript/jalview.js" language="javascript"></script>
 112 <script src="javascript/jvcontroller.js"> </script>
 113
 114
 115
 116 </head>
 117
 118
 119
 120 <div id="header"></div>
 121 <section id="section-content" class="section section-content">
 122         <div id="zone-content-wrapper"
 123                 class="zone-wrapper zone-content-wrapper clearfix">
 124
 125                 <div id="zone-content" class="zone zone-content clearfix container-12">
 126                         <!— — — — — — — — — — — side bar — — — — — — — — — — —>
 127                         <aside class="grid-3 region region-sidebar-first"
 128                                 id="region-sidebar-first">
 129                                 <div class="region-inner region-sidebar-first-inner">
 130                                         <section
 131                                                 class="block block-menu-block block-1 block-menu-block-1 odd"
 132                                                 id="block-menu-block-1">
 133                                                 <div class="block-inner clearfix">
 134                                                         <h2 class="block-title">
 135                                                                 <a href="/development" class="development active-trail">Development</a>
 136                                                         </h2>
 137                                                         <div class="content clearfix">
 138                                                                 <div class="menu-block-wrapper menu-block-1 menu-name-main-menu parent-mlid-0 menu-level-2">
 139                                                                     <div id="nav" class="nav">nav</div>
 140                                                                 </div>
 141                                                         </div>
 142                                                 </div>
 143                                         </section>
 144                                         <section
 145                                                 class="block block-menu-block block-2 block-menu-block-2 even"
 146                                                 id="block-menu-block-2">
 147                                                 <div class="block-inner clearfix">
 148                                                         <h2 class="block-title">
 149                                                                 <a href="/About" class="active-trail active">About</a>
 150                                                         </h2>
 151
 152                                                         <div class="content clearfix">
 153                                                                 <div
 154                                                                         class="menu-block-wrapper menu-block-2 menu-name-main-menu parent-mlid-0 menu-level-2">
 155                                                                         <div id="nav" class="nav">nav</div>
 156                                                                 </div>
 157                                                         </div>
 158                                                 </div>
 159                                         </section>
 160                                 </div>
 161                         </aside>
 162                         <!- — - - - - - - - - - - - - end of sidebar — — — — —>
 163
 164                         <div class="grid-9 region region-content" id="region-content">
 165                                 <div class="region-inner region-content-inner">
 166                                         <a id="main-content"></a>
 167                                         <div
 168                                                 class="block block-system block-main block-system-main odd block-without-title"
 169                                                 id="block-system-main">
 170                                                 <div class="block-inner clearfix">
 171                                                         <div class="content clearfix">
 172                                                                 <article about="/About" typeof="sioc:Item foaf:Document"
 173                                                                         class="node node-basic-page node-published node-not-promoted node-not-sticky author-admin odd clearfix"
 174                                                                         id="node-basic-page-18">
 175                                                                         <div class="content clearfix">
 176                                                                                 <div
 177                                                                                         class="field field-name-body field-type-text-with-summary field-label-hidden">
 178                                                                                         <div class="field-items">
 179                                                                                                 <div class="field-item even" property="content:encoded">
 180                                                                                                 <div id="content">
 181
 182
 183
 184
 185
 186
 187
 188 <div>
 189
 190
 191 <script language="JavaScript">
 192 // instead of this, we use a custom JmolApplet spec
 193 // jmolInitialize('jmol');
 194 jmolInitialize("","JmolApplet-14.2.14_2015.06.11.jar");
 195 </script>
 196 <script>
 197  var loglevel=1;
 198  function dbg(lvl,string) {
 199   if (_console && lvl<=loglevel) {_console.value += string + "\n";}
 200  }
 201  var _lastTime=new Date();
 202  var _path;
 203  var _datazip;
 204  var _zip;
 205  var alignA;
 206  var alignB;
 207  var featuresA;
 208  var featuresB;
 209  var pairs;
 210  var atompairs;
 211  var structdata;
 212  var jmolview;
 213  var jvstructassoc;
 214  var modeltofiles = new Array();
 215
 216  function lJvA() {
 217   jvfollower = document.getElementById("jvA");
 218   setConsole(document.getElementById("stdout"));
 219   linkJvJmol(jvfollower, "jmolView", modeltofiles);
 220  };
 221
 222  var _jvA=new Object();
 223  _jvA.attributes = {
 224   code : 'jalview.bin.JalviewLite',
 225   archive : 'jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar',
 226   width : '500',
 227   height : '350',
 228   mayscript : 'True',
 229   scriptable: 'True',
 230   id : 'jvA'
 231  };
 232  _jvA.parameters = {
 233    java_arguments : "-Xmx256m",
 234   externalstructureviewer : "true",
 235    oninit : "lJvA",
 236   automaticScrolling : "true",
 237 //  <!-- defaultColour : "Strand Propensity", -->
 238   file : "uniref50_mz.fa",
 239
 240   relaxedidmatch : "true",
 241   debug : "true",
 242   wrap : "false",
 243   // separator : "^",
 244   showAnnotation : "false",
 245   embedded : "true",
 246   showFullId : "false",
 247   RGB : "F2F2FF",
 248   linkLabel_1 : "EMBL-EBI Search",
 249   linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
 250   ,
 251   linkLabel_2 : "Uniprot"
 252   ,
 253   linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
 254   APPLICATION_URL : "http://www.jalview.org/services/launchApp",
 255   PDBfile : "1gaq.txt FER1_MAIZE",
 256   permissions : "sandbox"
 257  };
 258  jmolSetCallback("hoverCallback","_jmolhover");
 259   jmolSetCallback("pickCallback","_jmolpick");
 260   modeltofiles+="1gaq.txt";
 261 </script>
 262 <div style="width: 100%">
 263 <div style="width:35%; align:left; float:right;">
 264 <div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
 265 <p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-14.2.14_2015.06.11.jar">JmolApplet.jar</a>
 266 </p></div>
 267 </div>
 268 </div>
 269
 270 <!-- content template start -->
 271 <h2>Structure and Alignment</h2>
 272 <p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
 273
 274
 275 <div>
 276  <script>
 277   jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; background black; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;set hoverDelay 0.001; select 0","jmolView");
 278  </script>
 279 </div>
 280 <div>
 281 <applet
 282    code="jalview.bin.JalviewLite" width="500" height="350" id="jvA" mayscript="mayscript" archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar">
 283 <param name="permissions" value="sandbox"/>
 284 <param name="java_arguments" value="-Xmx256m"/>
 285 <param name="externalstructureviewer" value="true"/>
 286 <param name="oninit" value="lJvA"/>
 287 <param name="automaticScrolling" value="true"/>
 288 <param name="file" value="uniref50_mz.fa"/>
 289 <param name="relaxedidmatch" value="true"/>
 290 <param name="debug" value="true"/>
 291 <param name="wrap" value="false"/>
 292 <param name="showAnnotation" value="false"/>
 293 <param name="embedded" value="true"/>
 294 <param name="showFullId" value="false"/>
 295 <param name="RGB" value="F2F2FF"/>
 296 <param name="linkLabel_1" value="EMBL-EBI Search"/>
 297 <param name="linkUrl_1" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
 298 <param name="linkLabel_2" value="Uniprot"/>
 299 <param name="linkUrl_2" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
 300 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
 301 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
 302 </applet>
 303
 304 </div>
 305
 306 <!-- content template end -->
 307
 308
 309 </div>
 310
 311
 312
 313
 314
 315
 316
 317
 318
 319
 320 </div>
 321                                                                                                 </div>
 322                                                                                         </div>
 323                                                                                 </div>
 324                                                                         </div>
 325                                                                         <div class="clearfix">
 326                                                                                 <nav class="links node-links clearfix"></nav>
 327                                                                         </div>
 328                                                                 </article>
 329                                                         </div>
 330                                                 </div>
 331                                         </div>
 332                                 </div>
 333                         </div>
 334                 </div>
 335         </div>
 336 </section>
 337
 338 <div id="footer"></div>
 339
 340