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index.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="description" content="Spacewalk built with Vitejs" />
<title>Spacewalk</title>
<link rel="icon" href="./favicon.ico" />
<!-- Bootstrap 5.3.3 CSS -->
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css">
<!-- jQuery UI CSS -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.13.2/themes/base/jquery-ui.min.css"/>
<!-- Spectrum colorpicker CSS -->
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/spectrum.min.css">
<!-- DataTables CSS -->
<link rel="stylesheet" href="https://cdn.datatables.net/v/dt/dt-1.10.20/sl-1.3.1/datatables.min.css"/>
<!-- Font Awesome -->
<!-- Douglass Turner personal Font Awesome account -->
<script src="https://kit.fontawesome.com/534c6029c1.js" crossorigin="anonymous"></script>
<!-- jQuery JS -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.0/jquery.min.js"></script>
<!-- jQuery UI JS -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/jqueryui/1.13.2/jquery-ui.min.js"></script>
<!-- Bootstrap 5.3.3 JS -->
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/bootstrap.bundle.min.js"></script>
<!-- Dropbox Chooser API - sw_aiden_lab - supports aidenlab.org and netlify.app -->
<script src="https://www.dropbox.com/static/api/2/dropins.js" id="dropboxjs" data-app-key="dmf9qrwim29nbad"></script>
<!-- Datatables JS -->
<script src="https://cdn.datatables.net/v/dt/dt-1.10.20/sl-1.3.1/datatables.min.js"></script>
<!-- Google Platform JS -->
<script src="https://apis.google.com/js/platform.js"></script>
<!-- Spacewalk app entrypoint -->
<script type="module" src="./js/app.js"></script>
</head>
<body>
<nav class="navbar fixed-top py-0 navbar-expand-sm navbar-dark bg-dark justify-content-between" style="display: none;">
<div class="navbar-brand text-center align-middle">
Spacewalk
</div>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#spacewalk-navbar-content">
<span class="navbar-toggler-icon"></span>
</button>
<div id="spacewalk-navbar-content" class="collapse navbar-collapse d-flex flex-row">
<ul class="navbar-nav">
<!-- Fullscreen Button -->
<li class="nav-item">
<div class="ms-2 mt-1">
<button id="spacewalk-fullscreen-button" title="Fullscreen" type="button" class="btn nav-link">
Fullscreen
</button>
</div>
</li>
<!-- Spacewalk Files -->
<li class="nav-item">
<div class="dropdown ms-2 mt-1">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown">
File
</a>
<ul id="spacewalk-file-dropdown" class="dropdown-menu">
<!-- Ensemble Group -->
<li>
<button id="spacewalk-ensemble-group-select-button" class="dropdown-item" type="button" data-bs-toggle="modal" data-bs-target="#spacewalk-ensemble-group-select-modal">
Load Ensemble Group ...
</button>
</li>
<!-- Selection List -->
<li>
<button id="spacewalk-sw-load-select-button" class="dropdown-item" type="button" data-bs-toggle="modal" data-bs-target="#spacewalk-sw-load-select-modal">
Load From List ...
</button>
</li>
<!-- Local Files -->
<li>
<label class="dropdown-item btn btn-default btn-file">
<div>
<div>
Load Local File ...
</div>
<div>
<input id="spacewalk-sw-load-local-input" type="file" name="file" style="display: none;">
</div>
</div>
</label>
</li>
<!-- Dropbox -->
<li>
<div class="dropdown-item">
<div id="spacewalk-sw-dropbox-button" class="igv-app-dropdown-item-cloud-storage">
<div>Load Dropbox File ...</div>
<div>
<img src="img/dropbox-dropdown-menu-item.png" width="18" height="18">
</div>
</div>
</div>
</li>
<!-- Google Drive -->
<li>
<div class="dropdown-item">
<div id="spacewalk-sw-google-drive-button" class="igv-app-dropdown-item-cloud-storage">
<div>Load Google Drive File ...</div>
<div><img src="img/googledrive-dropdown-menu-item.png" width="18" height="18"></div>
</div>
</div>
</li>
<!-- URL -->
<li>
<button id="spacewalk-sw-load-url-button" class="dropdown-item" type="button" data-bs-toggle="modal" data-bs-target="#spacewalk-sw-load-url-modal">
Load URL ...
</button>
</li>
</ul>
</div>
</li>
<!-- trace-select widget -->
<div class="ms-2 input-group">
<input type="text" class="form-control text-center" id="spacewalk_trace_select_input">
<div class="input-group-append">
<button id="spacewalk_trace_select_button_minus" class="btn btn-light btn-sm" type="button"><i class="fas fa-minus"></i></button>
<button id="spacewalk_trace_select_button_plus" class="btn btn-light btn-sm" type="button"><i class="fas fa-plus"></i></button>
</div>
</div>
<!-- Share (generate URL) -->
<li class="nav-item">
<div class="ms-2 mt-1">
<a id="igv-app-share-button" href="#" class="nav-link" data-bs-toggle="modal" data-bs-target="#igv-app-share-modal">
Share
</a>
</div>
</li>
<!-- Session -->
<li class="nav-item">
<div class="dropdown ms-2 mt-1">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown">
Session
</a>
<div id="spacewalk-session-dropdown-menu" class="dropdown-menu">
<!-- Session 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="igv-app-dropdown-local-session-file-input" type="file" name="file" style="display: none;">
</div>
</div>
</label>
<!-- Session Dropbox -->
<!-- Session Google Drive -->
<!-- Session URL -->
<button class="dropdown-item" type="button" data-bs-toggle="modal" data-bs-target="#spacewalk-session-url-modal">
Load URL ...
</button>
<div class="dropdown-divider"></div>
<!-- Save Session Local file -->
<button class="dropdown-item" type="button" data-bs-toggle="modal" data-bs-target="#spacewalk-session-save-modal">
Save ...
</button>
</div>
</div>
</li>
<!-- View -->
<li class="nav-item">
<div class="dropdown ms-2 mt-1">
<a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown">
View
</a>
<ul id="spacewalk-viewers-dropdown-menu" class="dropdown-menu checkbox-menu allow-focus">
<!-- IGV Viewer -->
<li>
<label>
<input id="spacewalk_ui_manager_ui_controls_igv" data-target="spacewalk_igv_panel" type="checkbox">
Show IGV
</label>
</li>
<!-- Juicebox Viewer -->
<li>
<label>
<input id="spacewalk_ui_manager_ui_controls_juicebox" data-target="spacewalk_juicebox_panel" type="checkbox">
Show Juicebox
</label>
</li>
</ul>
</div>
</li>
<!-- About -->
<li class="nav-item">
<div class="ms-2 mt-1">
<button id="spacewalk-about-button" title="About" type="button" class="btn nav-link" data-bs-toggle="popover" data-bs-placement="bottom" data-bs-html="true">
About
</button>
</div>
</li>
<!-- Help -->
<li class="nav-item">
<div class="ms-2 mt-1">
<button id="spacewalk-help-button" title="Help" type="button" class="btn nav-link" data-bs-toggle="popover" data-bs-placement="bottom" data-bs-html="true">
Help
</button>
</div>
</li>
</ul>
</div>
</nav>
<main id="spacewalk-main" role="main">
<div id="spacewalk-root-container">
<!-- Render Settings Button -->
<div id="spacewalk-threejs-settings-button-container">
<button id="spacewalk-threejs-settings-button" type="button" class="btn btn-default">
<i class="fas fa-cog fa-lg"></i>
</button>
</div>
<!-- Render Settings Panel -->
<div id="spacewalk_ui_manager_panel" class="card" style="display: none;">
<ul class="list-group list-group-flush">
<!-- PointCloud render style -->
<li id="spacewalk_ui_manager_pointcloud_render_style" class="list-group-item">
<!-- Point Size-->
<div id="spacewalk_ui_manager_pointcloud_point_size">
<div id="spacewalk_ui_manager_pointcloud_point_size_label">
Point Size
</div>
<div>
<i class="fas fa-minus-circle"></i>
</div>
<div>
<i class="fas fa-plus-circle"></i>
</div>
</div>
<!-- Point Transparency -->
<div id="spacewalk_ui_manager_pointcloud_point_transparency">
<div>
Point Transparency
</div>
<div>
<i class="fas fa-minus-circle"></i>
</div>
<div>
<i class="fas fa-plus-circle"></i>
</div>
</div>
</li>
<!-- Ball & Stick and Ribbon render styles -->
<li id="spacewalk_ui_manager_render_styles" class="list-group-item">
<div>
<div class="form-check">
<input name="spacewalk-render-style" id="spacewalk-render-style-ball-stick" class="form-check-input" type="radio" checked>
<label class="form-check-label" for="spacewalk-render-style-ball-stick">Ball & Stick</label>
</div>
<div id="spacewalk-ball-radius-control" class="spacewalk-ball-stick-control">
<div>
Ball Radius
</div>
<div>
<i class="fas fa-minus-circle"></i>
<i class="fas fa-plus-circle"></i>
</div>
</div>
<div id="spacewalk-stick-radius-control" class="spacewalk-ball-stick-control">
<div>
Stick Radius
</div>
<div>
<i class="fas fa-minus-circle"></i>
<i class="fas fa-plus-circle"></i>
</div>
</div>
<div class="form-check">
<input name="spacewalk-render-style" id="spacewalk-render-style-ribbon" class="form-check-input" type="radio">
<label class="form-check-label" for="spacewalk-render-style-ribbon">Ribbon</label>
</div>
</div>
</li>
<!-- Ground Plane -->
<li class="list-group-item spacewalk-colorpicker-li">
<div class="input-group">
<div class="input-group-text">
<input id="spacewalk_ui_manager_groundplane" type="checkbox">
</div>
<div class="input-group-text">Ground Plane</div>
<div class="input-group-text" data-colorpicker="groundplane"></div>
</div>
</li>
<!-- Axes (Gnomon) -->
<li class="list-group-item spacewalk-colorpicker-li">
<div class="input-group">
<div class="input-group-text">
<input id="spacewalk_ui_manager_gnomon" type="checkbox">
</div>
<span class="input-group-text">Axes</span>
<div class="input-group-text" data-colorpicker="gnomon"></div>
</div>
</li>
<!-- Background -->
<li class="list-group-item spacewalk-colorpicker-li">
<div class="input-group">
<div class="input-group-text">
<input id="spacewalk_ui_manager_input_group_shim" type="checkbox">
</div>
<span class="input-group-text">Background</span>
<div class="input-group-text" data-colorpicker="background"></div>
</div>
</li>
</ul>
</div>
<!-- Info Panel -->
<div id="spacewalk_info_panel" style="display:none;">
<!-- ensemble group -->
<div>
<div>
ENSEMBLE GROUP
</div>
<div id="spacewalk_info_panel_ensemble_group" style="display: none;">
-
</div>
</div>
<!-- genome -->
<div>
<div>
GENOME:
</div>
<div id="spacewalk_info_panel_genome">
-
</div>
</div>
<!-- locus -->
<div>
<div>
LOCUS:
</div>
<div id="spacewalk_info_panel_locus">
-
</div>
</div>
</div>
<!-- three-js container -->
<div id="spacewalk-threejs-container">
<!-- drag handle -->
<div id="spacewalk-threejs-drag-container">
<i class="fas fa-lg fa-grip-horizontal"></i>
</div>
<!-- three-js canvas | trace-navigator -->
<div id="spacewalk-threejs-trace-navigator-container">
<!-- three-js canvas container -->
<div id="spacewalk-threejs-canvas-container">
<div id="spacewalk-threejs-canvas-center-dot" style="display: none;"></div>
</div>
<!-- trace navigator -->
<div id="spacewalk-trace-navigator-container">
<!-- header -->
<div id="spacewalk-trace-navigator-header"></div>
<!-- widget -->
<div id="spacewalk-trace-navigator-widget">
<canvas id="spacewalk_color_ramp_canvas_highlight"></canvas>
<canvas id="spacewalk_color_ramp_canvas_rgb"></canvas>
<canvas id="spacewalk_color_ramp_canvas_alpha"></canvas>
</div>
<!-- footer -->
<div id="spacewalk-trace-navigator-footer"></div>
</div>
</div>
</div>
<!-- general purpose spinner -->
<div class="spacewalk-spinner-container d-flex justify-content-center align-items-center" style="background-color:transparent;">
<div id="spacewalk-spinner" class="spinner-border text-secondary" style="display:none; width: 8rem; height: 8rem;"></div>
</div>
<!-- juicebox panel -->
<div id="spacewalk_juicebox_panel" class="card">
<div class="card-header px-0">
<div class="spacewalk_card_drag_container">
<i class="fas fa-square-full"></i>
<i class="fas fa-times-circle" data-target="spacewalk_ui_manager_ui_controls_juicebox"></i>
</div>
<ul class="nav nav-tabs" role="tablist">
<li class="nav-item" role="presentation">
<button id="spacewalk-juicebox-panel-hic-map-tab" class="nav-link" data-bs-toggle="tab" data-bs-target="" type="button" role="tab">Hi-C Map</button>
</li>
<li class="nav-item" role="presentation">
<button id="spacewalk-juicebox-panel-live-map-tab" class="nav-link" data-bs-toggle="tab" data-bs-target="" type="button" role="tab">Live Contact</button>
</li>
<li class="nav-item" role="presentation">
<button id="spacewalk-juicebox-panel-live-distance-map-tab" class="nav-link" data-bs-toggle="tab" data-bs-target="" type="button" role="tab">Live Distance</button>
</li>
</ul>
<ul class="list-group list-group-flush">
<!-- Hi-C map file chooser -->
<li id="hic-file-chooser-dropdown" class="list-group-item mx-auto py-1 ps-1">
<div class="dropdown">
<button id="hic-contact-map-dropdown" class="btn btn-sm btn-outline-secondary dropdown-toggle" type="button" data-bs-toggle="dropdown">
Load Hi-C Map
</button>
<ul class="dropdown-menu">
<!-- ENCODE Maps -->
<li>
<button class="dropdown-item" id="hic-encode-hosted-contact-map-presentation-button" type="button" data-bs-toggle="modal" data-bs-target="#hic-encode-hosted-contact-map-modal">
Load ENCODE Maps ...
</button>
</li>
<!-- Local Map File -->
<li>
<label class="dropdown-item btn btn-default btn-file">
<div class="igv-app-dropdown-item-cloud-storage">
<div>
Load Local Map File ...
</div>
<div>
<input name="contact-map" type="file" style="display: none;">
</div>
</div>
</label>
</li>
<!-- Dropbox -->
<li>
<div class="dropdown-item">
<div id="hic-contact-map-dropdown-dropbox-button" class="igv-app-dropdown-item-cloud-storage">
<div>Load Dropbox Map File ...</div>
<div>
<img src="img/dropbox-dropdown-menu-item.png" width="18" height="18">
</div>
</div>
</div>
</li>
<!-- Google Drive -->
<li>
<div class="dropdown-item">
<div id="hic-contact-map-dropdown-google-drive-button" class="igv-app-dropdown-item-cloud-storage">
<div>Load Google Drive Map File ...</div>
<div><img src="img/googledrive-dropdown-menu-item.png" width="18" height="18"></div>
</div>
</div>
</li>
<!-- URL -->
<li>
<a class="dropdown-item" href="#" data-bs-toggle="modal" data-bs-target="#hic-load-url-modal">
Load Map URL ...
</a>
</li>
</ul>
</div>
</li>
<!-- Live Contact Map Threshold Widget -->
<li id="hic-live-contact-frequency-map-threshold-widget" class="list-group-item py-1 ps-1">
<div class="d-flex justify-content-between align-items-center">
<div class="input-group input-group-sm">
<div class="input-group-text">Threshold</div>
<input id="spacewalk_contact_frequency_map_adjustment_select_input" type="text" class="form-control text-center">
<button id="hic-live-contact-frequency-map-threshold-button" class="btn btn-secondary" type="button">Enter</button>
</div>
<button id="hic-live-contact-frequency-map-calculation-button" class="btn btn-sm btn-outline-secondary" type="button">Calculate Live Map</button>
</div>
</li>
<!-- Live Distance Map Toggle Widget -->
<li id="hic-live-distance-map-toggle-widget" class="list-group-item py-1 px-1">
<div class="form-group d-flex justify-content-between align-items-center">
<div class="btn-group btn-group-toggle" data-toggle="buttons">
<label class="btn btn-sm btn-outline-secondary">
<input type="radio" name="options" id="spacewalk-live-distance-map-toggle-ensemble" autocomplete="off"> Ensemble
</label>
<label class="btn btn-sm btn-outline-secondary">
<input type="radio" name="options" id="spacewalk-live-distance-map-toggle-trace" autocomplete="off"> Trace
</label>
</div>
<button id="hic-calculation-live-distance-button" type="button" class="btn btn-sm btn-outline-secondary ms-2">Calculate Live Map</button>
</div>
</li>
</ul>
</div>
<div class="card-body p-0">
<!-- juicebox browser container -->
<div id="spacewalk_juicebox_root_container"></div>
</div>
</div>
<!-- igvjs panel -->
<div id="spacewalk_igv_panel" class="card">
<div id="spacewalk_igv_container" class="card-body">
<!-- drag handle -->
<div class="spacewalk_card_drag_container">
<i class="fas fa-square-full"></i>
<div class="dropdown">
<a class="dropdown-toggle" data-bs-toggle="dropdown">
IGV File
</a>
<ul id="spacewalk-track-dropdown-menu" class="dropdown-menu">
<!-- Local File -->
<li>
<label class="dropdown-item btn btn-default btn-file">
<div class="igv-app-dropdown-item-cloud-storage">
<div>
Load Local File ...
</div>
<div>
<input id="hic-local-track-file-input" name="local-track-file" type="file" style="display: none;">
</div>
</div>
</label>
</li>
<!-- Dropbox -->
<li>
<div class="dropdown-item">
<div id="spacewalk-track-dropbox-button" class="igv-app-dropdown-item-cloud-storage">
<div>Load Dropbox File ...</div>
<div>
<img src="img/dropbox-dropdown-menu-item.png" width="18" height="18">
</div>
</div>
</div>
</li>
<!-- Google Drive -->
<li>
<div class="dropdown-item">
<div id="spacewalk-track-dropdown-google-drive-button" class="igv-app-dropdown-item-cloud-storage">
<div>Load Google Drive File ...</div>
<img src="img/googledrive-dropdown-menu-item.png" width="18" height="18">
</div>
</div>
</li>
<!-- URL -->
<li>
<a class="dropdown-item" href="#" data-bs-toggle="modal" data-bs-target="#spacewalk-track-load-url-modal">Load URL ...</a>
</li>
<div id="hic-annotations-section" class="dropdown-divider"></div>
</ul>
</div>
<i class="fas fa-times-circle" data-target="spacewalk_ui_manager_ui_controls_igv"></i>
</div>
<!-- igv browser container -->
<div id="spacewalk_igv_root_container"></div>
</div>
</div>
</div>
<!-- Share URL Modal -->
<div id="igv-app-share-modal" class="modal fade">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<div id="igv-app-share-input-modal-close-button" class="modal-title">Share</div>
<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></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="igv-app-share-input" type="text" class="form-control" placeholder="">
</div>
</div>
<div class="col-sm-2">
<button id="igv-app-copy-link-button" type="button" class="btn btn-sm btn-default">
COPY
</button>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</main>
<!-- About button content -->
<div id="spacewalk-about-button-content" style="display: none;">
<p>
The Spacewalk browser is a project at the <a href="https://aidenlab.org/" target="_blank">Aiden Lab</a> as part of the NSF Center for Theoretical Biological Physics
and the NIH Center for Genome Imaging.
</p>
<p>
The lead developer of Spacewalk is Doug Turner. The application development team includes Dimos Gkountaroulis,
Olga Dudchenko, and Guy Nir.
</p>
<p>
The Spacewalk browser uses a custom .sw file format. This format was developed in collaboration with the laboratory of Jose Onuchic,
and it's development was led by Vinicius Contessoto, Matheus Mello, Antonio Oliveira Junior, Jim Robinson, and Doug Turner. More information
on the file format is available <a href="https://github.com/turner/sw2swb/wiki/The-Spacewalk-Binary-File-Format" target="_blank">here</a>
</p>
</div>
<!-- Help button content -->
<div id="spacewalk-help-button-content" style="display: none;">
<!-- Docuumentation -->
<p>
<a href="https://github.com/igvteam/spacewalk/blob/master/README.md" target="_blank">Documentation</a>
</p>
<!-- Github Code -->
<p>
<a href="https://github.com/igvteam/spacewalk" target="_blank">Github Repository</a>
</p>
<!-- File Format -->
<p>
<a href="https://github.com/turner/sw2swb/wiki/The-Spacewalk-Binary-File-Format" target="_blank">File Format</a>
</p>
<!-- Issues -->
<p>
<a href="https://github.com/igvteam/spacewalk/issues" target="_blank">Issues</a>
</p>
<!-- Release Number-->
<p id="spacewalk-help-menu-release">
</p>
</div>
</body>
</html>