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index.html
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<!DOCTYPE HTML>
<html>
<head>
<title>xiNET | Examples</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<meta name="description" content="xiNET is a visualisation tool for cross-linking and mass spectrometry data." />
<meta name="keywords" content="xiNET, biologists, mass-spectrometrists, cross-linking, protein, complexes, 3d, models, rappsilber, software" />
<meta name="viewport" content="initial-scale=1, maximum-scale=1">
<meta name="apple-mobile-web-app-capable" content="yes">
<meta name="apple-mobile-web-app-status-bar-style" content="black">
<link rel="icon" type="image/ico" href="images/logos/favicon.ico">
<link rel="stylesheet" href="./demo/css/reset.css" />
<link rel="stylesheet" href="./demo/css/noscript.css" />
<link rel="stylesheet" href="./demo/css/style.css" />
<link rel="stylesheet" href="./demo/css/noNav.css" />
<link rel="stylesheet" href="./demo/css/xiNET.css">
<!--
<script type="text/javascript" src="./xiNET_2.0.0.js"></script>
-->
<!--libraries-->
<script type="text/javascript" src="./vendor/d3.js"></script>
<script type="text/javascript" src="./vendor/colorbrewer.js"></script>
<script type="text/javascript" src="./vendor/FileSaver.js"></script>
<script type="text/javascript" src="./vendor/rgbcolor.js"></script>
<!--xiNET-->
<script type="text/javascript" src="./src/controller/Init.js"></script>
<script type="text/javascript" src="./src/controller/MouseEvents.js"></script>
<script type="text/javascript" src="./src/controller/Layout.js"></script>
<script type="text/javascript" src="./src/controller/Refresh.js"></script>
<script type="text/javascript" src="./src/controller/ToolTips.js"></script>
<script type="text/javascript" src="./src/model/Match.js"></script>
<script type="text/javascript" src="./src/model/Link.js"></script>
<script type="text/javascript" src="./src/model/Protein.js"></script>
<script type="text/javascript" src="./src/model/Annotation.js"></script>
<script type="text/javascript" src="./src/model/ProteinLink.js"></script>
<script type="text/javascript" src="./src/model/ResidueLink.js"></script>
<script type="text/javascript" src="./src/controller/ExternalControls.js"></script>
<script type="text/javascript" src="./src/controller/Rotator.js"></script>
<script type="text/javascript" src="./src/controller/xiNET_Storage.js"></script>
<script type="text/javascript" src="./src/controller/ReadCSV.js"></script>
<script type="text/javascript" src="./src/controller/Fasta.js"></script>
</head>
<body>
<!-- Slidey panels -->
<div class="overlay-box" id="infoPanel">
<div id="networkCaption">
<p>No selection.</p>
</div>
</div>
<div class="overlay-box" id="helpPanel">
<table class="overlay-table" bordercolor="#eee" >
<tr>
<td>Toggle the proteins between a bar and a circle</td>
<td>Click on protein</td>
</tr>
<tr>
<td>Zoom</td>
<td>Mouse wheel</td>
</tr>
<tr>
<td>Pan</td>
<td>Click and drag on background</td>
</tr>
<tr>
<td>Move protein</td>
<td>Click and drag on protein</td>
</tr>
<tr>
<td>Expand bar <br>(increases bar length until sequence is visible)</td>
<td>Shift_left-click on protein</td>
</tr>
<tr>
<td>Rotate bar</td>
<td>Click and drag on handles that appear at end of bar</td>
</tr>
<tr>
<td>Hide/show protein (and all links to it)</td>
<td>Right-click on protein</td>
</tr>
<tr>
<td>Hide links between two specific proteins</td>
<td>Right click on any link between those proteins</td>
</tr>
<tr>
<td>Show all hidden links</td>
<td>Right click on background</td>
</tr>
<tr>
<td>'Flip' self-links</td>
<td>Right-click on self-link</td>
</tr>
</table>
</div>
<div class="overlay-box" id="legendPanel">
<div><img src="./demo/images/fig3_1.svg"></div>
</div>
<script type="text/javascript">
//<![CDATA[
helpShown = false;
infoShown = false;
legendShown = false;
function toggleHelpPanel() {
if (helpShown){
hideHelpPanel();
}
else {
showHelpPanel();
}
}
function toggleInfoPanel() {
if (infoShown){
hideInfoPanel();
}
else {
showInfoPanel();
}
}
function toggleLegendPanel() {
if (legendShown){
hideLegendPanel();
}
else {
showLegendPanel();
}
}
function showHelpPanel() {
helpShown = true;
d3.select("#helpPanel").transition().style("height", "500px").style("top", "100px").duration(700);
}
function hideHelpPanel() {
helpShown = false;
d3.select("#helpPanel").transition().style("height", "0px").style("top", "-95px").duration(700);
}
function showInfoPanel() {
infoShown = true;
d3.select("#infoPanel").transition().style("height", "300px").style("bottom", "115px").duration(700);
}
function hideInfoPanel() {
infoShown = false;
d3.select("#infoPanel").transition().style("height", "0px").style("bottom", "-95px").duration(700);
}
function showLegendPanel() {
legendShown = true;
d3.select("#legendPanel").transition().style("height", "500px").style("top", "100px").duration(700);
}
function hideLegendPanel() {
legendShown = false;
d3.select("#legendPanel").transition().style("height", "0px").style("top", "-95px").duration(700);
}
//]]>
</script>
<!-- Main -->
<div id="main">
<div class="container">
<h1 class="page-header">Example:
<select class="btn btn-1 btn-1a" id="dataSets" onchange="loadData();" >
<!--
<option value="TFIIF">TFIIF</option>
-->
<option selected value="PolII">PolII</option>
<option value="PP2A">PP2A</option>
<option value="NPC">NPC</option>
</select>
<div style='float:right'>
<button class="btn btn-1 btn-1a network-control resetzoom" onclick="xlv.reset();">
Reset
</button>
<button class="btn btn-1 btn-1a network-control" onclick="xlv.exportSVG('networkSVG');">Export SVG</button>
<label class="btn">
Legend
<input id="selection" onclick="toggleLegendPanel()" type="checkbox">
</label>
<label class="btn">
Details
<input id="selection" onclick="toggleInfoPanel()" type="checkbox">
</label>
<label class="btn">
Help
<input id="help" onclick="toggleHelpPanel()" type="checkbox">
</label>
</div>
</h1>
</div>
<div class="long-citation" id="citation"></div>
<div id="networkContainer"></div>
<div class="controlsexamplespage">
<label>Self-Links
<input checked="checked"
id="selfLinks"
onclick="xlv.showSelfLinks(document.getElementById('selfLinks').checked)"
type="checkbox"
/>
</label>
<label> Ambig.
<input checked="checked"
id="ambig"
onclick="xlv.showAmbig(document.getElementById('ambig').checked)"
type="checkbox"
/>
</label>
<div id="scoreSlider">
<p class="scoreLabel" id="scoreLabel1"></p>
<input id="slide" type="range" min="0" max="100" step="1" value="0" oninput="sliderChanged()"/>
<p class="scoreLabel" id="scoreLabel2"></p>
<p id="cutoffLabel">(cut-off)</p>
</div> <!-- outlined scoreSlider -->
<div style='float:right'>
<label>Annot.
<select id="annotationsSelect" onChange="changeAnnotations();">
<option selected='selected'>Custom</option>
<option>UniprotKB</option>
<option>SuperFamily</option>
<option>None</option>
</select>
</label>
</div>
</div>
<script type="text/javascript">
//<![CDATA[
var sliderDecimalPlaces = 1;
function getMinScore(){
if (xlv.scores){
var powerOfTen = Math.pow(10, sliderDecimalPlaces);
return (Math.floor(xlv.scores.min * powerOfTen) / powerOfTen)
.toFixed(sliderDecimalPlaces);
}
}
function getMaxScore(){
if (xlv.scores){
var powerOfTen = Math.pow(10, sliderDecimalPlaces);
return (Math.ceil(xlv.scores.max * powerOfTen) / powerOfTen)
.toFixed(sliderDecimalPlaces);
}
}
function sliderChanged(){
var slide = document.getElementById('slide');
var powerOfTen = Math.pow(10, sliderDecimalPlaces);
var cut = ((slide.value / 100)
* (getMaxScore() - getMinScore()))
+ (getMinScore() / 1);
cut = cut.toFixed(sliderDecimalPlaces);
var cutoffLabel = document.getElementById("cutoffLabel");
cutoffLabel.innerHTML = '(' + cut + ')';
xlv.setCutOff(cut);
}
//]]>
</script>
</div> <!-- MAIN -->
<script type="text/javascript">
//<![CDATA[
var config = [
//~ {//TFIIF
//~ file:"./data/TFIIF.csv",
//~ cite:"<p>Data from <a href='http://www.nature.com/emboj/journal/v29/n4/full/emboj2009401a.html' target='_blank'>Chen ZA, Jawhari A, Fischer L, Buchen C, Tahir S, Kamenski T, Rasmussen M, Lariviere L, Bukowski-Wills J-C, Nilges M, Cramer P & Rappsilber J (2010) Architecture of the RNA polymerase II–TFIIF complex revealed by cross-linking and mass spectrometry. The EMBO Journal 29: 717–726</a>.</p>"
//~ },
{//PolII
file:"./demo/data/PolII.csv",
cite:"<p>Data from <a href='http://www.nature.com/emboj/journal/v29/n4/full/emboj2009401a.html' target='_blank'>Chen ZA, Jawhari A, Fischer L, Buchen C, Tahir S, Kamenski T, Rasmussen M, Lariviere L, Bukowski-Wills J-C, Nilges M, Cramer P & Rappsilber J (2010) Architecture of the RNA polymerase II–TFIIF complex revealed by cross-linking and mass spectrometry. The EMBO Journal 29: 717–726</a>.</p>",
customAnnot:"./demo/data/TFIIF_annot.csv"
},
{//PP2A
file:"./demo/data/PP2A.csv",
cite:"<p>Data from <a href='http://www.sciencemag.org/content/337/6100/1348' target='_blank'>Herzog, F., Kahraman, A., Boehringer, D., Mak, R., Bracher, A., Walzthoeni, T., Leitner, A., Beck, M., Hartl, F.-U., Ban, N., Malmstrom, L., and Aebersold, R. (2012) Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry. Science 337, 1348–1352</a>.</p>"
},
{//NPC
file:"./demo/data/NPC.csv",
cite:"<p>Data from <a href='http://www.sciencedirect.com/science/article/pii/S0092867413014165' target='_blank'>Bui, K. H., von Appen, A., DiGuilio, A. L., Ori, A., Sparks, L., Mackmull, M.-T., Bock, T., Hagen, W., Andrés-Pons, A., Glavy, J. S., and Beck, M. (2013) Integrated Structural Analysis of the Human Nuclear Pore Complex Scaffold. Cell 155, 1233–1243</a>.</p>"
}
];
function loadData(){
var dataSetsSelect = document.getElementById('dataSets');
var path = config[dataSetsSelect.selectedIndex].file;
document.getElementById('citation').innerHTML = config[dataSetsSelect.selectedIndex].cite;
if (config[dataSetsSelect.selectedIndex].customAnnot){
d3.text(config[dataSetsSelect.selectedIndex].customAnnot, "text/csv", function(annot) {
d3.text(path, "text/csv", function(text) {
xlv.clear();
xlv.readCSV(text, null, annot);
initSlider();
});
});
}
else {
d3.text(path, "text/csv", function(text) {
xlv.clear();
xlv.readCSV(text);
initSlider();
});
}
}
//~ window.addEventListener('load', function() {
var targetDiv = document.getElementById('networkContainer');
xlv = new xiNET.Controller(targetDiv);
var targetDiv = document.getElementById('networkContainer');
var messageDiv = document.getElementById('networkCaption');
xlv = new xiNET.Controller(targetDiv);
xlv.setMessageElement(messageDiv);
loadData();
changeAnnotations();
xlv.showSelfLinks(document.getElementById('selfLinks').checked);
xlv.showAmbig(document.getElementById('ambig').checked);
//~ }, false);
function changeAnnotations(){
var annotationSelect = document.getElementById('annotationsSelect');
xlv.setAnnotations(annotationSelect.options[annotationSelect.selectedIndex].value);
};
function initSlider(){
if (xlv.scores === null){
d3.select('#scoreSlider').style('display', 'none');
}
else {
document.getElementById('scoreLabel1').innerHTML = "Score:" + getMinScore();
document.getElementById('scoreLabel2').innerHTML = getMaxScore();
sliderChanged();
d3.select('#scoreSlider').style('display', 'inline-block');
}
};
//]]>
</script>
</body>
</html>