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VQI_GenomeBrowser/VQI_GenomeBrowserDemo.html
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<html> | |
<head> | |
<script src="http://d3js.org/d3.v3.min.js"></script> | |
<script src="http://code.jquery.com/jquery-1.10.2.min.js"></script> | |
<script src="../VQI_Publisher.js"></script> | |
<script src="VQI_GenomeBrowser.js"></script> | |
<script src="FileSaver.min.js"></script> | |
<script src="jquery.qtip.min.js"></script> | |
<link href="jquery.qtip.min.css" rel="stylesheet" type="text/css" /> | |
<!-- Latest compiled and minified CSS --> | |
<!-- <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"> --> | |
<link rel="stylesheet" href="bootstrap.min.css"> | |
<link rel="stylesheet" href="menu.css"> | |
<!-- Latest compiled and minified JavaScript --> | |
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/js/bootstrap.min.js"></script> | |
</head> | |
<body> | |
<div id="test"> | |
</div> | |
<div id="test2"> | |
</div> | |
<footer> | |
<script type="text/javascript"> | |
var obj = new VQI_GenomeBrowser("test",'dynamic_loading.php'); | |
//insert path to file and indexfile | |
/*obj.addTrack([], "fasta", "fasta", | |
{ file : "/Users/corywang/Downloads/hg19.fa.txt", | |
indexFile : "/Users/corywang/Downloads/hg19.fa.fai.txt"}); | |
obj.addTrack([], "cpg", "cpg", | |
{fileHandle : "upload1437097194,upload1437098473,upload1437098556"}); | |
obj.addTrack([], "HG19", "bed", {fileHandle : "upload1436481988"}); | |
obj.addTrack([], "Tile2 Content Snp", "bed", | |
{ fileHandle : "upload1436411775", | |
exportable : true});*/ | |
var genomes = { | |
"HG19":{ | |
/*fasta: {fasta: "../../genome/hg19.fa", index: "../../genome/hg19.fa.fai"}, | |
genes: {file: "../../genome/hg19_genes.txt", table_name:'hg19_gene_annotation'}, | |
cpg: {file: "../../genome/hg19_genes.txt", table_name:'hg19_cpg'},*/ | |
//fasta: {fasta: "/Users/corywang/Downloads/hg19.fa.txt", index : "/Users/corywang/Downloads/hg19.fa.fai.txt"}, | |
genes: {file: "hg19_refgene.txt", table_name: "hg19_refgene"}, | |
cpg: {file: "cpg_site_hg19.txt,shelve_hg19.txt,shoer_hg19.txt", table_name: "cpg_site_hg19,shelve_hg19,shoer_hg19"}, | |
//custom: {file: "", table_name:'upload1436411775'} | |
}, | |
// "MM9":{ | |
// fasta: {fasta: "/Users/corywang/Downloads/mm9.fa.txt", index: "/Users/corywang/Downloads/mm9.fa.fai.txt"}, | |
// //genes: {file: "../../genome/mm9/mm9_genes.txt", table_name:'mm9_gene_annotation'}, | |
// // gene_annotation: {label: 'mm9', table_name:'mm9_gene_annotation'}, | |
// }, | |
}; | |
obj.loadGenomes(genomes); //loads the genomes based on the datastructure described above | |
setTimeout(function(){ hs()}, 3000); | |
function hs (){ | |
obj.setGenome("HG19"); | |
} | |
//obj.setGenome("HG19"); | |
// obj.setGenome("MM9"); //should set hg19 genome in dropdown and display fasta, cpg and genes tracks. | |
// addTrack(); should add track using the data array supplied. | |
</script> | |
</footer> | |
</body> | |
</html> | |