2 <header><title>BioJS viewer</title></header>
5 <!-- include MSA js + css -->
6 <script src="https://s3-eu-west-1.amazonaws.com/biojs/msa/latest/msa.js"></script>
7 <link type=text/css rel=stylesheet href=https://s3-eu-west-1.amazonaws.com/biojs/msa/latest/msa.css />
10 <!-- optional: menubar -->
11 <link type=text/css rel=stylesheet href= https://raw.githubusercontent.com/greenify/biojs-vis-msa/master/external/jquery.dropdown.css />
13 <div id="menuDiv"></div>
14 <div> This data was generated from Jalview<div>
15 <div id="yourDiv">press "Run with JS"</div>
16 <input type='hidden' id='seqData' name='seqData' value='#sequenceData#'/>
21 <script src=//cdn.biojs-msa.org/msa/0.2/msa.min.gz.js></script>
24 // this is a way how you use a bundled file parser
25 biojs.io.clustal.read("http://www.corsproxy.com/rostlab.org/~goldberg/jalv_example.clustal", function(seqs){
29 // set your custom properties
30 // @see: https://github.com/greenify/biojs-vis-msa/tree/master/src/g
34 //alert(document.getElementById("seqData").value);
36 opts.seqs = JSON.parse(document.getElementById("seqData").value);
38 //opts.seqs = seqs; //msa.utils.seqgen.getDummySequences(1000,300);
39 opts.el = document.getElementById("yourDiv");
40 opts.vis = {conserv: false, overviewbox: false};
41 opts.zoomer = {alignmentHeight: 225, labelWidth: 130,labelFontsize: "13px",labelIdLength: 20, menuFontsize: "12px",menuMarginLeft: "3px", menuPadding: "3px 4px 3px 4px", menuItemFontsize: "14px", menuItemLineHeight: "14px"};
44 var m = new msa.msa(opts);
46 // the menu is independent to the MSA container
48 menuOpts.el = document.getElementById('div');
50 var defMenu = new msa.menu.defaultmenu(menuOpts);
51 m.addView("menu", defMenu);
53 // call render at the end to display the whole MSA