JAL-2629 fix expected length error for hmmbuild by uniquifying sequences
[jalview.git] / examples / embeddedWJmol.html
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123
124
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126 <script src="jmol/Jmol2.js"></script>
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128 <script src="javascript/jquery.timer.js"></script>
129 <script src="javascript/jquery.blockUI.js"></script>
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132 <script src="javascript/jvcontroller.js"> </script>
133
134        
135
136 </head>
137
138
139
140 <div id="header"></div>
141 <section id="section-content" class="section section-content">
142         <div id="zone-content-wrapper"
143                 class="zone-wrapper zone-content-wrapper clearfix">
144
145                 <div id="zone-content" class="zone zone-content clearfix container-12">
146                         <!— — — — — — — — — — — side bar — — — — — — — — — — —>
147                         <aside class="grid-3 region region-sidebar-first"
148                                 id="region-sidebar-first">
149                                 <div class="region-inner region-sidebar-first-inner">
150                                         <section
151                                                 class="block block-menu-block block-1 block-menu-block-1 odd"
152                                                 id="block-menu-block-1">
153                                                 <div class="block-inner clearfix">
154                                                         <h2 class="block-title">                                                                
155                                                                 <a href="/development" class="development active-trail">Development</a>
156                                                         </h2>
157                                                         <div class="content clearfix">
158                                                                 <div class="menu-block-wrapper menu-block-1 menu-name-main-menu parent-mlid-0 menu-level-2">
159                                                                     <div id="nav" class="nav">nav</div>
160                                                                 </div>
161                                                         </div>
162                                                 </div>
163                                         </section>
164                                         <section
165                                                 class="block block-menu-block block-2 block-menu-block-2 even"
166                                                 id="block-menu-block-2">
167                                                 <div class="block-inner clearfix">
168                                                         <h2 class="block-title">
169                                                                 <a href="/About" class="active-trail active">About</a>
170                                                         </h2>
171
172                                                         <div class="content clearfix">
173                                                                 <div
174                                                                         class="menu-block-wrapper menu-block-2 menu-name-main-menu parent-mlid-0 menu-level-2">
175                                                                         <div id="nav" class="nav">nav</div>
176                                                                 </div>
177                                                         </div>
178                                                 </div>
179                                         </section>
180                                 </div>
181                         </aside>
182                         <!- — - - - - - - - - - - - - end of sidebar — — — — —>
183
184                         <div class="grid-9 region region-content" id="region-content">
185                                 <div class="region-inner region-content-inner">
186                                         <a id="main-content"></a>
187                                         <div
188                                                 class="block block-system block-main block-system-main odd block-without-title"
189                                                 id="block-system-main">
190                                                 <div class="block-inner clearfix">
191                                                         <div class="content clearfix">
192                                                                 <article about="/About" typeof="sioc:Item foaf:Document"
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198                                                                                         <div class="field-items">
199                                                                                                 <div class="field-item even" property="content:encoded">
200                                                                                                 <div id="content">
201
202
203
204
205
206
207
208 <div>
209   
210
211 <script language="JavaScript">
212 // instead of this, we use a custom JmolApplet spec
213 // jmolInitialize('jmol');
214 jmolInitialize("","JmolApplet-14.6.4_2016.10.26.jar");
215 </script>
216 <script>
217  var loglevel=1;
218  function dbg(lvl,string) {
219   if (_console && lvl<=loglevel) {_console.value += string + "\n";}
220  }
221  var _lastTime=new Date();
222  var _path;
223  var _datazip;
224  var _zip;
225  var alignA;
226  var alignB;
227  var featuresA;
228  var featuresB;
229  var pairs;
230  var atompairs;
231  var structdata;
232  var jmolview;
233  var jvstructassoc;
234  var modeltofiles = new Array();
235
236  function lJvA() {
237   jvfollower = document.getElementById("jvA");
238   setConsole(document.getElementById("stdout"));
239   linkJvJmol(jvfollower, "jmolView", modeltofiles);
240  };
241
242  var _jvA=new Object();
243  _jvA.attributes = {
244   code : 'jalview.bin.JalviewLite',
245   archive : 'jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar',
246   width : '500',
247   height : '350',
248   mayscript : 'True',
249   scriptable: 'True',
250   id : 'jvA'
251  };
252  _jvA.parameters = {
253    java_arguments : "-Xmx256m",
254   externalstructureviewer : "true",
255    oninit : "lJvA",
256   automaticScrolling : "true",
257 //  <!-- defaultColour : "Strand Propensity", -->
258   file : "uniref50_mz.fa",
259   
260   relaxedidmatch : "true",
261   debug : "true",
262   wrap : "false",
263   // separator : "^",
264   showAnnotation : "false",
265   embedded : "true",
266   showFullId : "false",
267   RGB : "F2F2FF",
268   linkLabel_1 : "EMBL-EBI Search",
269   linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
270   ,
271   linkLabel_2 : "Uniprot"
272   ,
273   linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
274   APPLICATION_URL : "http://www.jalview.org/services/launchApp",
275   PDBfile : "1gaq.txt FER1_MAIZE",
276   permissions : "sandbox"
277  };
278  jmolSetCallback("hoverCallback","_jmolhover");
279   jmolSetCallback("pickCallback","_jmolpick");
280   modeltofiles+="1gaq.txt";
281 </script> 
282 <div style="width: 100%">
283
284 </div>
285
286 <!-- content template start -->
287 <h2>Structure and Alignment</h2>
288 <p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
289
290
291 <div>
292  <script>
293   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");
294  </script>
295 </div>
296 <div>
297 <applet
298    code="jalview.bin.JalviewLite" width="500" height="350" id="jvA" mayscript="mayscript" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
299 <param name="permissions" value="sandbox"/>
300 <param name="java_arguments" value="-Xmx256m"/>
301 <param name="externalstructureviewer" value="true"/>
302 <param name="oninit" value="lJvA"/>
303 <param name="automaticScrolling" value="true"/>
304 <param name="file" value="uniref50_mz.fa"/>
305 <param name="relaxedidmatch" value="true"/>
306 <param name="debug" value="true"/>
307 <param name="wrap" value="false"/>
308 <param name="showAnnotation" value="false"/>
309 <param name="embedded" value="true"/>
310 <param name="showFullId" value="false"/>
311 <param name="RGB" value="F2F2FF"/>
312 <param name="linkLabel_1" value="EMBL-EBI Search"/>
313 <param name="linkUrl_1" value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"/>
314 <param name="linkLabel_2" value="Uniprot"/>
315 <param name="linkUrl_2" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$"/>
316 <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp"/>
317 <param name="PDBfile" value="1gaq.txt FER1_MAIZE"/>
318 </applet>
319
320 </div>
321
322 <!-- content template end -->
323
324  
325 </div>
326
327
328
329
330
331
332
333
334
335
336 </div>
337                                                                                                 </div>
338                                                                                         </div>
339                                                                                 </div>
340                                                                         </div>
341                                                                         <div class="clearfix">
342                                                                                 <nav class="links node-links clearfix"></nav>
343                                                                         </div>
344                                                                 </article>
345                                                         </div>
346                                                 </div>
347                                         </div>
348                                 </div>
349                         </div>
350                 </div>
351         </div>
352 </section>
353
354 <div id="footer"></div>
355
356