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index.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>IGV-JB</title>
<!-- Bootstrap 4 CSS -->
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css">
<!-- DataTables CSS -->
<!-- <link rel="stylesheet" href="//cdn.datatables.net/1.10.20/css/jquery.dataTables.min.css"/>-->
<link rel="stylesheet" type="text/css"
href="https://cdn.datatables.net/v/dt/dt-1.10.20/sl-1.3.1/datatables.min.css"/>
<!-- Bootstrap 4 and Dependancies -->
<script src="https://code.jquery.com/jquery-3.3.1.slim.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.7/umd/popper.min.js"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js"></script>
<!-- Datatables JS -->
<!-- <script src="//cdn.datatables.net/1.10.20/js/jquery.dataTables.min.js"></script>-->
<script type="text/javascript" src="https://cdn.datatables.net/v/dt/dt-1.10.20/sl-1.3.1/datatables.min.js"></script>
<!-- Font Awesome CSS-->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css">
<!-- Juicebox CSS-->
<link rel="stylesheet" type="text/css" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/juicebox.css">
</head>
<body>
<h2>Demonstration of Juicebox <-> IGV interaction</h2>
<ul>
<li>Navigation is synched</li>
<li>Cross hairs in JB => vertical bars in IGV (hold shift key down and move mouse over JB for crosshairs)</li>
<li>Click "Update Contacts" to send juicebox contact records with significant counts to IGV, represented as arcs.
</li>
</ul>
<main id="hic-main" class="container-fluid">
<nav class="navbar navbar-expand-lg navbar-light bg-light ">
<!-- Contact Map -->
<div class="dropdown">
<button id="hic-contact-map-dropdown" class="btn btn-outline-dark btn-sm ml-2 dropdown-toggle" type="button"
data-toggle="dropdown">
Load Map
</button>
<div id="hic-contact-map-dropdown-menu" class="dropdown-menu">
<!-- Select -->
<a class="dropdown-item" href="#" data-toggle="modal" data-target="#hic-contact-map-modal">
Juicebox Archive ...</a>
<!-- ENCODE hosted maps -->
<button id="hic-encode-hosted-contact-map-presentation-button" class="dropdown-item"
type="button" data-toggle="modal" data-target="#hic-encode-hosted-contact-map-modal">ENCODE ...
</button>
<!-- Local Map File -->
<label class="dropdown-item btn btn-default btn-file">
<div class="igv-app-dropdown-item-cloud-storage">
<div>
Local File ...
</div>
<div>
<input id="contact-map-local" name="contact-map" type="file" style="display: none;">
</div>
</div>
</label>
<!-- URL -->
<a class="dropdown-item" href="#" data-toggle="modal" data-target="#hic-load-url-modal">URL ...</a>
</div>
</div>
<!-- Track -->
<div class="dropdown">
<button id="hic-track-dropdown-button" class="btn btn-outline-dark btn-sm ml-2 dropdown-toggle"
type="button"
data-toggle="dropdown">
Load Tracks
</button>
<div id="hic-track-dropdown-menu" class="dropdown-menu">
<button id="encode-signal-tracks-button" class="dropdown-item"
type="button" data-toggle="modal" data-target="#encode-signal-tracks-modal">ENCODE Signals ...
</button>
<button id="encode-other-tracks-button" class="dropdown-item"
type="button" data-toggle="modal" data-target="#encode-other-tracks-modal">ENCODE Other ...
</button>
<!-- Local File -->
<label class="dropdown-item btn btn-default btn-file">
<div class="igv-app-dropdown-item-cloud-storage">
<div>
Local File ...
</div>
<div>
<input id="track-file-input" name="local-track-file" type="file"
style="display: none;">
</div>
</div>
</label>
<a class="dropdown-item" href="#" data-toggle="modal" data-target="#track-load-url-modal">URL ...</a>
</div>
</div>
<!-- Share -->
<div title="Share">
<button id="share-button" class="btn btn-outline-dark btn-sm ml-2" type="button" data-toggle="modal"
data-target="#app-share-modal">
Share
</button>
</div>
<button id="projectButton" class="btn btn-outline-dark btn-sm ml-5">Update Contacts</button>
</nav>
<!-- App container -->
<div class="row">
<div class="col-md-12">
<!-- app + caption container-->
<div id="app-caption" class="juicebox-app-caption-container">
<div style="display:flex">
<div id="jbDiv"></div>
<div id="igvDiv" style="flex-grow:0;flex-shrink:0;flex-basis: 950px"></div>
</div>
<!-- caption -->
<div id="hic-caption" class="hic-caption-container" contenteditable="true">
</div>
</div>
</div>
</div>
<!-- Other dialogs -->
<div id="hic-load-url-modal" class="modal fade">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<div class="modal-title">Load URL</div>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<div class="form-group">
<input type="text" class="form-control" placeholder="Enter URL">
</div>
</div>
</div>
</div>
</div>
<div id="track-load-url-modal" class="modal fade">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<div class="modal-title">Load URL</div>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<div class="form-group">
<input type="text" class="form-control" placeholder="Enter URL">
</div>
</div>
</div>
</div>
</div>
<!-- Share URL Modal -->
<div id="app-share-modal" class="modal fade">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<div id="app-share-input-modal-close-button" class="modal-title">Share</div>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<div class="container-fluid">
<!-- copy url -->
<div class="row">
<div class="col-sm-8">
<div class="form-group">
<input id="app-share-input" type="text" class="form-control" placeholder="">
</div>
</div>
<div class="col-sm-2">
<button id="app-copy-link-button" type="button" class="btn btn-sm btn-default">
COPY
</button>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div style="width:600px;margin-top: 10px;margin-bottom: 10px">
<h3>Contact Parameters</h3>
<div class="form-group">
<label for="binThresholdInput">Off diagonal bin threshold</label>
<input type="text" class="form-control" id="binThresholdInput" aria-describedby="binThresholdHelp" placeholder="10" value="10">
<small id="binThresholdHelp" class="form-text text-muted">Contacts close to diagonal (abs(binX-binY) < threshold) are filtered. </small>
</div>
<div class="form-group">
<label for="percentileThresholdInput">Percentile threshold</label>
<input type="text" class="form-control" id="percentileThresholdInput" aria-describedby="percentileThresholdHelp" placeholder="2" value="2">
<small id="percentileThresholdHelp" class="form-text text-muted">Contacts with counts in top "percentile thresold" are kept. Value range 0-100. </small>
</div>
<div class="form-group">
<label for="alphaModifierInput">Alpha modifier</label>
<input type="text" class="form-control" id="alphaModifierInput" aria-describedby="alphaModifierHelp" placeholder="0.5" value="0.5">
<small id="alphaModifierHelp" class="form-text text-muted">Use to adjust color intensity of IGV arcs. Value range 0-1 Default = 0.5 </small>
</div>
<button type="button" class="btn btn-outline-dark btn-sm ml-2" id="contactParametersButton">Update Contacts</button>
</div>
</main>
<script type="module">
//import {init} from "./js/init.js"
import {init} from "./dist/igv-juicebox.js"
init({
jbContainer: document.getElementById("jbDiv"),
igvContainer: document.getElementById("igvDiv"),
projectContactsButton: document.getElementById("projectButton"),
contactsParametersButton: document.getElementById("contactParametersButton")
})
</script>
</body>
</html>