1 <!-- boiler plate link to alternate demopage -->
5 <!--//--><![CDATA[//><!--
6 var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
9 <script src="javascript/deployJava.js"></script>
10 <script src="jmol/Jmol.js"></script>
11 <script src="javascript/jquery-1.4.4.min.js"></script>
12 <script src="javascript/jquery.timer.js"></script>
13 <script src="javascript/jquery.blockUI.js"></script>
14 <script src="javascript/jshashtable-2.1.js" language="javascript"></script>
16 <script src="javascript/jalview.js" language="javascript"></script>
17 <script language="JavaScript">
18 // instead of this, we use a custom JmolApplet spec
19 // jmolInitialize('jmol');
20 jmolInitialize("","JmolApplet-12.2.4.jar");
23 var s1 = "ml:i@midd..", s2 = "atelcpoueau", s3 = "iomyob.neck", href="";
25 { href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i);
31 function dbg(lvl,string) {
32 if (_console && lvl<=loglevel) {_console.value += string + "\n";}
34 var _lastTime=new Date();
47 var modeltofiles = new Array();
50 jvfollower = document.getElementById("jvA");
51 setConsole(document.getElementById("stdout"));
53 sep = jvfollower.getSeparator();
54 //jvapp.setSeparator(""+jvapp.getSeparator());
55 linkJvJmol(jvfollower, "jmolView", modeltofiles);
58 var _jvA=new Object();
60 code : 'jalview.bin.JalviewLite',
61 archive : 'jalviewApplet.jar,JmolApplet-12.2.4.jar',
69 java_arguments : "-Xmx256m",
70 externalstructureviewer : "true",
72 automaticScrolling : "true",
73 // <!-- defaultColour : "Strand Propensity", -->
74 file : "uniref50_mz.fa",
76 relaxedidmatch : "true",
80 showAnnotation : "false",
84 linkLabel_1 : "EMBL-EBI Search",
85 linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"
87 linkLabel_2 : "Uniprot"
89 linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
90 APPLICATION_URL : "http://www.jalview.org/services/launchApp",
91 PDBfile : "1gaq.txt FER1_MAIZE",
92 permissions : "sandbox"
94 jmolSetCallback("hoverCallback","_jmolhover");
95 jmolSetCallback("pickCallback","_jmolpick");
96 modeltofiles+="1gaq.txt";
100 <div style="width: 100%">
101 <div style="width:35%; align:left; float:right;">
102 <div style="margin:8px; padding:10px; border: 2px solid black; align: left;">
103 <p>Quick Links to jars for example:<br/><a href="jalviewApplet.jar">jalviewApplet.jar</a> and <a href="JmolApplet-12.2.4.jar">JmolApplet.jar</a>
108 <!-- content template start -->
109 <h2>Structure and Alignment</h2>
110 <p>This demo shows how JalviewLite and Jmol can be integrated with the JalviewLite javascript library.</p>
113 jmolApplet("500x500","zap; load FILE '1gaq.txt'; frame 0; select all; wireframe off; spacefill off; cartoons; restrict; center *; set selectionhalos true;select 0","jmolView");
116 deployJava.runApplet(_jvA.attributes, _jvA.parameters, '1.4');
119 <!-- content template end -->