JAL-2920 wrap description in <html/> if it includes <br/>
[jalview.git] / examples / embeddedWJmol.html
1 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML+RDFa 1.1//EN">
2 <!--
3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
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19  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
20  * The Jalview Authors are detailed in the 'AUTHORS' file.
21  -->
22  <html lang="en" dir="ltr" version="HTML+RDFa 1.1"
23         xmlns:content="http://purl.org/rss/1.0/modules/content/"
24         xmlns:dc="http://purl.org/dc/terms/"
25         xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:og="http://ogp.me/ns#"
26         xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
27         xmlns:sioc="http://rdfs.org/sioc/ns#"
28         xmlns:sioct="http://rdfs.org/sioc/types#"
29         xmlns:skos="http://www.w3.org/2004/02/skos/core#"
30         xmlns:xsd="http://www.w3.org/2001/XMLSchema#">
31 <head profile="http://www.w3.org/1999/xhtml/vocab">
32 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
33 <link rel="shortcut icon"
34         href="http://www.jalview.org/sites/all/themes/jalview/favicon.ico"
35         type="image/vnd.microsoft.icon" />
36 <meta name="viewport"
37         content="width=device-width, initial-scale=1, maximum-scale=1, minimum-scale=1, user-scalable=no" />
38 <meta content="" about="/About" property="dc:title" />
39 <link rel="shortlink" href="/node/18" />
40 <meta name="Generator" content="Drupal 7 (http://drupal.org)" />
41 <link rel="canonical" href="/About" />
42 <title>Development | jalview.org</title>
43 <link type="text/css" rel="stylesheet"
44         href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_pbm0lsQQJ7A7WCCIMgxLho6mI_kBNgznNUWmTWcnfoE.css"
45         media="all" />
46 <link type="text/css" rel="stylesheet"
47         href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_gUtVu-PFpNy2iKRzspQnPE665qK-eDx99tAc6O2EKBs.css"
48         media="all" />
49 <link type="text/css" rel="stylesheet"
50         href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_HByEx9XzXH_VOfr3lfyJmXRKhQdq8UyyslSu9odJFaw.css"
51         media="all" />
52 <link type="text/css" rel="stylesheet"
53         href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_Rj_Ai4KdTE0qt75bSUOfQPNak90tBSJRVjZIjglGhlM.css"
54         media="all" />
55
56 <!--[if lte IE 6]>
57 <link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/all/themes/jalview/css/ie6.css?nqc8th" media="all" />
58 <![endif]-->
59
60 <!--[if lte IE 7]>
61 <link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/all/themes/jalview/css/ie7.css?nqc8th" media="all" />
62 <![endif]-->
63
64 <!--[if lte IE 8]>
65 <link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/all/themes/jalview/css/ie8.css?nqc8th" media="all" />
66 <![endif]-->
67
68 <!--[if (lt IE 9)&(!IEMobile)]>
69 <link type="text/css" rel="stylesheet" href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_ybf1eloQwwauLFbDPh5-J2RvDVEM4Gsh1NsAC0ynfNs.css" media="all" />
70 <![endif]-->
71
72 <!--[if gte IE 9]><!-->
73 <link type="text/css" rel="stylesheet"
74         href="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/css/css_kD8qBi2CLfQkl16-SgdHuwlYq_NUjXsjCxmpeidlT0I.css"
75         media="all" />
76 <!--<![endif]-->
77 <script type="text/javascript">
78 <!--//--><![CDATA[//><!--
79         document.cookie = 'adaptive_image=' + Math.max(screen.width, screen.height)
80                         + '; path=/';
81         //--><!]]>
82 </script>
83 <script type="text/javascript"
84         src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_0gj6QcpfRH2jzTbCQqf7kEkm4MXY0UA_sRhwPc8jC1o.js"></script>
85 <script type="text/javascript"
86         src="http://www.jalview.org/sites/all/modules/lightbox2/js/lightbox.js?1434966756"></script>
87 <script type="text/javascript"
88         src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_SoFDHsgxDY2cLYbZ6HeW4SLlU_sLxsgGT6tSFwfsHGY.js"></script>
89 <script type="text/javascript"
90         src="http://www.jalview.org/sites/all/modules/mobile_navigation/js/mobile_menu.js?nqc8th"></script>
91 <script type="text/javascript"
92         src="http://www.jalview.org/sites/all/modules/mobile_navigation/mobile_navigation.js?nqc8th"></script>
93 <script type="text/javascript"
94         src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_IDBX5SzkJ9gGNq7x-qOE_2DZsexqguTJQGMKvi4w-Uw.js"></script>
95 <script type="text/javascript">
96 <!--//--><![CDATA[//><!--
97         var _gaq = _gaq || [];
98         _gaq.push([ "_setAccount", "UA-9060947-1" ]);
99         _gaq.push([ "_trackPageview" ]);
100         (function() {
101                 var ga = document.createElement("script");
102                 ga.type = "text/javascript";
103                 ga.async = true;
104                 ga.src = ("https:" == document.location.protocol ? "https://ssl"
105                                 : "http://www")
106                                 + ".google-analytics.com/ga.js";
107                 var s = document.getElementsByTagName("script")[0];
108                 s.parentNode.insertBefore(ga, s);
109         })();
110         //--><!]]>
111 </script>
112 <script type="text/javascript"
113         src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_tnUY-Xr0uSK3E1mkrZ6ON7OmxH4PiVjShebnFJ8E-9c.js"></script>
114 <script type="text/javascript"
115         src="http://www.jalview.org/sites/jalview.aegir-prod-6.lifesci.dundee.ac.uk/files/js/js_43n5FBy8pZxQHxPXkf-sQF7ZiacVZke14b0VlvSA554.js"></script>
116
117 <script type="text/javascript">
118 <!--//--><![CDATA[//><!--
119 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120 //--><!]]>
121 </script>
122 <!--[if lt IE 9]><script src="http://html5shiv.googlecode.com/svn/trunk/html5.js"></script><![endif]-->
123
124
125 <script src="javascript/deployJava.js"></script>
126 <script src="jmol/Jmol2.js"></script>
127 <script src="javascript/jquery-1.4.4.min.js"></script>
128 <script src="javascript/jquery.timer.js"></script>
129 <script src="javascript/jquery.blockUI.js"></script>
130 <script src="javascript/jshashtable-2.1.js" language="javascript"></script>
131 <script src="javascript/jalview.js" language="javascript"></script>
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"
193                                                                         class="node node-basic-page node-published node-not-promoted node-not-sticky author-admin odd clearfix"
194                                                                         id="node-basic-page-18">
195                                                                         <div class="content clearfix">
196                                                                                 <div
197                                                                                         class="field field-name-body field-type-text-with-summary field-label-hidden">
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