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index.html
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<!DOCTYPE html>
<html lang='en'>
<head>
<title>context-aware-phylogenetic-trees</title>
<meta charset="utf-8">
<link rel="stylesheet" href="https://netdna.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css">
<link rel="stylesheet" href="https://netdna.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap-theme.min.css">
<link href="https://netdna.bootstrapcdn.com/font-awesome/4.0.3/css/font-awesome.css" rel="stylesheet">
<link rel='stylesheet' href='https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css'>
<link rel="stylesheet" href="styles/style.css">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/default.min.css">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.0/jquery.min.js"></script>
<script src="https://netdna.bootstrapcdn.com/bootstrap/3.3.5/js/bootstrap.min.js"></script>
<script src="https://d3js.org/d3.v3.min.js"></script>
<!-- <script src="scripts/main.js" ></script> -->
<script src="scripts/phylotree.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/highlight.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/underscore.js/1.8.3/underscore-min.js"></script>
</head>
<body>
<header>
<h1>Context Aware Phylogenetic Trees</h1>
<nav>
<a href="https://doi.org/10.3389/fgene.2022.891240">Link to paper</a>
<a href="https://github.com/ghattab/CAPT">Fork me on GitHub</a>
</nav>
</header>
<div id="buttonsContainer" class="buttonsAll">
<div class="buttonsLeftDiv">
<button name="fileInput" id="fileInput2" class="buttonsLeft" onclick="document.getElementById('fileInput').click()">Upload Tree (nwk)</button>
<input type="file" id="fileInput" accept="text/plain" multiple="multiple" style="display:none"/>
<select id="treeSelection" class="selectionLeft">
<option value="None">Select Tree</option>
<option value="c_Methanomicrobia">(Archaea) Class Methanomicrobia</option>
<option value="p_Hadarchaeota">(Archaea) Phylum Hadarchaeota</option>
<option value="f__Actinomycetaceae">(Bacteria) Family Actinomycetaceae</option>
<option value="f__Shewanellaceae">(Bacteria) Family Shewanellaceae</option>
</select>
<button id="createTree" class="buttonsLeft">Create Tree View</button>
<!-- <button id="toggleBTN" onclick='toggleBtn()' class="buttonsLeft">Show Toolbar</button> -->
<button id="select_all" class="buttonsLeft">Select All</button>
</div>
<div id=buttonsIcicle class="buttonsRightDiv">
<select id="domainSelection" class="selectionRight">
<option value="None">Select Domain</option>
<option value="archaea" selected>Archaea</option>
<option value="bacteria">Bacteria</option>
</select>
<button id="createTaxonomy" class="buttonsRight">Create Taxonomy View</button>
</div>
</div>
<div id="svgContainer" class="containerViews">
<div id="treeContainer" class="container">
<div id = 'toolBar'class = 'row'>
<div class = 'col-md-12'>
<div class="btn-toolbar" role="toolbar">
<div class="btn-group">
<button type="button" class="btn btn-default btn-sm" data-direction = 'vertical' data-amount = '1' title = "Expand vertical spacing">
<i class="fa fa-arrows-v" ></i>
</button>
<button type="button" class="btn btn-default btn-sm" data-direction = 'vertical' data-amount = '-1' title = "Compress vertical spacing">
<i class="fa fa-compress fa-rotate-135" ></i>
</button>
<button type="button" class="btn btn-default btn-sm" data-direction = 'horizontal' data-amount = '1' title = "Expand horizonal spacing">
<i class="fa fa-arrows-h" ></i>
</button>
<button type="button" class="btn btn-default btn-sm" data-direction = 'horizontal' data-amount = '-1' title = "Compress horizonal spacing">
<i class="fa fa-compress fa-rotate-45" ></i>
</button>
<button type="button" class="btn btn-default btn-sm" id = "sort_ascending" title = "Sort deepest clades to the bototm">
<i class="fa fa-sort-amount-asc" ></i>
</button>
<button type="button" class="btn btn-default btn-sm" id = "sort_descending" title = "Sort deepsest clades to the top">
<i class="fa fa-sort-amount-desc" ></i>
</button>
<button type="button" class="btn btn-default btn-sm" id = "sort_original" title = "Restore original order">
<i class="fa fa-sort" ></i>
</button>
<div class="btn-group" data-toggle="buttons">
<label class="btn btn-default active btn-sm">
<input type="radio" class = "phylotree-align-toggler" data-align = "left" name="options-align" autocomplete="off" title = "Align tips labels to branches">
<i class="fa fa-align-left" ></i>
</input>
</label>
<label class="btn btn-default btn-sm">
<input type="radio" class = "phylotree-align-toggler" data-align = "right" name="options-align" autocomplete="off" title = "Align tips labels to the edge of the plot">
<i class="fa fa-align-right" ></i>
</input>
</label>
</div>
</div>
<div class="btn-group">
<button type="button" class="btn btn-default btn-sm" id = "select_all" title = "Restore original order">
Select All
</button>
<!-- <button type="button" class="btn-group-radio" id = "select_all" onclick = 'selectAllBtn()' title = "Select all">
Select All
</button>
<button type="button" class="btn-group-radio" id = "unselect_all" title = "Unselect All">
Unselect All
</button> -->
<!-- <label class="btn btn-default active btn-sm">
<input type="" name="options" id = "select_all" data-mode = "select" autocomplete="off" title = "Select all" onclick="selectAllElements()"> Select All
</label> -->
<!-- <label class="btn btn-default btn-sm">
<input type="radio" name="options" class = "select-unselect-mode" data-mode = "unselect" autocomplete="off" title = "Unselect all"> Unselect All
</label> -->
</div>
</div>
</div>
</div>
<svg id="tree_display"></svg>
</div>
<div id="containerIcicle" class="containerIcicle">
</div>
</div>
<!-- <footer>
<p> Copyright | © <script>document.write(new Date().getFullYear())</script> CAPT</p>
</footer> -->
<script src="scripts/main.js" ></script>
<script type="text/javascript" src="scripts/d3-body.js"></script>
<script type="text/javascript">
var _paq = window._paq || [];
_paq.push(['trackPageView']);
_paq.push(['enableLinkTracking']);
(function() {
var u="https://webtrack.uni-marburg.de/";
_paq.push(['setTrackerUrl', u+'piwik.php']);
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g.type='text/javascript'; g.async=true; g.defer=true; g.src=u+'piwik.js'; s.parentNode.insertBefore(g,s);
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</script>
</body>
</html>