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example-one-liner.html
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example-one-liner.html
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<html>
<head>
<title>pViz example - one liner</title>
<link rel="stylesheet" type="text/css" href="deps/bootstrap.min.css">
<link rel="stylesheet" type="text/css" href="deps/pviz-core.css">
<script src="deps/pviz-bundle.min.js"></script>
<!-- just a few lines of javscript to decorate the page -->
<script src="examples-utils.js"></script>
</head>
<body class="container">
<div class="row">
<h2>pViz, a one-line example</h2>
</div>
<div class="row">
<div class="span6">
<table class="table table-bordered">
<thead>
<tr>
<th>id</th>
<th>secondary structures</th>
</tr>
</thead>
<tbody>
<td> HER2 head </td>
<td id="one-liner"></td>
</tbody>
</table>
</div>
</div>
<div class="row">
<h3>Comments</h3>
We define a SeqEntry object, map features on it and display it as a simple one-liner image.
There is no zoom nor interaction at this level, but we can display tons of such icons on a web page.
<br/>
It is possible to add a
<a href= "example-one-liner-multiple-categories.html"><code>
groups:['xxx','yyy',...]
</code>
</a>
option to the OneLiner constructor to keep only a set of features and display them on multiple lines
</div>
<script class="example">
//namespace handling pViz classes
var pviz = this.pviz;
/*
* Define the model, a sequence entry with an explicit sequence
* For this example, we don't actually need the sequence itself.
* Whatever string with the correct length is OK (ok, it's ugly, but it can be useful in certain cases)
*/
var seqEntry = new pviz.SeqEntry({
sequence : 'MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLA'
});
new pviz.OneLiner({
model : seqEntry,
el : '#one-liner'
}).render();
/*
* Features are added explicitely.
* There is only on group of features here (secondary_structure). There can be more that would be merged or we could keep only one group with the filer:'xxx' option
*
* In real application, these features would be read from DASReader, a PeffReader or whatever ajax call you find convenient (the view is rendered when model changes)
*/
seqEntry.addFeatures([{
category : 'secondary structure',
type : 'beta_strand',
start : 24,
end : 26
}, {
category : 'secondary structure',
type : 'helix',
start : 38,
end : 49
}, {
category : 'secondary structure',
type : 'beta_strand',
start : 53,
end : 57
}, {
category : 'secondary structure',
type : 'beta_strand',
start : 59,
end : 63
}, {
category : 'secondary structure',
type : 'helix',
start : 71,
end : 73
}, {
category : 'secondary structure',
type : 'beta_strand',
start : 78,
end : 81
}, {
category : 'secondary structure',
type : 'beta_strand',
start : 83,
end : 87
}, {
category : 'secondary structure',
type : 'beta_strand',
start : 91,
end : 94
}, {
category : 'secondary structure',
type : 'turn',
start : 108,
end : 110
}, {
category : 'secondary structure',
type : 'beta_strand',
start : 111,
end : 116
}, {
category : 'secondary structure',
type : 'turn',
start : 129,
end : 131
}, {
category : 'secondary structure',
type : 'beta_strand',
start : 138,
end : 140
}, {
category : 'secondary structure',
type : 'beta_strand',
start : 150,
end : 155
}]);
</script>
</body>
</html>