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index.php
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<?php
/*
* File: index.php
* Author Chanaka Mannapperuma
* Description: Main PHP for ComPlEX2
* Created: Thu May 15 09:28:04 GMT+02:00 2014
*/
// Extensions
require_once("service/extensions.php");
$ext = new Extension_Collection();
?>
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
<title>Complex</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="keywords" content="Complex 2.0">
<link rel="icon" type="image/png" href="favicon.ico">
<link rel="stylesheet" type="text/css" href="css/demo.css">
<link rel="stylesheet" type="text/css" href="css/style.css">
<link rel="stylesheet" type="text/css" href="https://cdn.datatables.net/v/dt/dt-1.10.16/b-1.5.1/b-html5-1.5.1/r-2.2.1/sc-1.4.4/sl-1.2.5/datatables.min.css">
<link rel="stylesheet" href="https://unpkg.com/cytoscape-panzoom@2.5.2/cytoscape.js-panzoom.css">
<link rel="stylesheet" href="https://unpkg.com/font-awesome@4.7.0/css/font-awesome.css">
<link href="css/complexmessage.min.css" media="screen" type="text/css" rel="stylesheet">
</head>
<body>
<div id="prebox" style="width:100%;height:400%;background-color:#FFF;z-index:5000000;position:absolute;top:0px;left:0px;vertical-align:middle" >
<div style="left:48%;top:48%" class="loader_color2 medium"></div>
</div>
<button class="floating-help" id="help-button">?</button>
<div id="documentation-fade" class="fade hide"></div>
<?php include("documentation.php") ?>
<header>
<img src="images/complex_logo.png" alt="Complex logo">
</header>
<div class="accordion">
<div class="accordion-head">
Input
</div>
<div class="accordion-content input-container">
<div id="network-selection-wrapper" class="input-group">
<div id="network-reference-border"></div>
<div id="network-reference-line"></div>
<template id="network-selection-template">
<div class="network-selection-item network-input">
<button class="network-selection-token"></button
><input class="network-selection-radio" type="radio" name="reference">
</div>
</template>
</div>
<div class="input-group">
<?php if ($config["genie"]["enabled"]): ?>
<div class="network-input">
<label for="genes-lists">Genes list</label>
<select id="genes-lists" size="7">
<option value="No network selected...">Load example</option>
</select>
</div>
<?php endif; ?>
<div class="network-input">
<?php if (!$config["genie"]["enabled"]): ?>
<div>
<?php endif; ?>
<label for="sink1">Genes</label>
<?php if (!$config["genie"]["enabled"]): ?>
<button class="btn btn-4" id="example-genelist-button">Load example</button>
</div>
<?php endif; ?>
<textarea name="sp1gene" id="sink1" rows="6" placeholder="<?php echo $config["genie"]["enabled"] ? "No network selected..." : "Enter gene IDs"; ?>"></textarea>
</div>
</div>
<div class="input-group">
<div class="network-input">
<label for="coexpressionThreshold">Co-expression threshold: ≥<span id="coexpressionThresholdDisplay">0.990</span></label>
<input id="coexpressionThreshold" type="range" min="0.95" max="1" step="0.001" value="0.99" name="coexpressionThreshold">
</div>
<div class="network-input">
<button id="align_to_species_button" class="btn btn-4 btn-4c">Align</button>
</div>
</div>
</div>
<?php if (!$ext->is_empty() && $config["extensions"]["enabled"]): ?>
<div class="accordion-head">
Extensions
</div>
<div class="accordion-content">
<div class="extension-control">
<?php foreach ($ext as $n=>$e): ?>
<div class="extension">
<input class="extension-checkbox" type="checkbox" id="<?php echo $e->id; ?>-extension-checkbox"
data-extension-name="<?php echo $n; ?>"
data-extension-id="<?php echo $e->id; ?>">
<label for="<?php echo $e->id; ?>-extension-checkbox"><?php echo $n ?></label>
<p><?php echo $e->description; ?>
<div class="extension-legend">
<strong>Legend:</strong>
<?php
$gene_style = $e->get_gene_style();
$edge_style = $e->get_edge_style();
?>
<?php foreach ($e->subextensions as $x): ?>
<div class="extension-legend-item">
<svg width="40px" height="20px" xmlns="http://www.w3.org/2000/svg">
<line class="edge" x1="0" y1="10" x2="30" y2="10" style="<?php echo isset($edge_style[$x->id]['line-color']) && !is_null($edge_style[$x->id]['line-color']) ? 'stroke: '.$edge_style[$x->id]['line-color'].';' : ''; ?><?php echo isset($edge_style[$x->id]['width']) && !is_null($edge_style[$x->id]['width']) ? 'stroke-width: '.$edge_style[$x->id]['width'].';' : '' ?><?php echo isset($edge_style[$x->id]['line-style']) && !is_null($edge_style[$x->id]['line-style']) && $edge_style[$x->id]['line-style'] === 'dashed' ? 'stroke-dasharray: 5,3;' : ''; ?>" />
<circle class="node" cx="30" cy="10" r="9" style="<?php echo isset($gene_style[$x->id]['background-color']) && !is_null($gene_style[$x->id]['background-color']) ? 'fill: '.$gene_style[$x->id]['background-color'].';' : ''; ?>" />
</svg>
<abbr title="<?php echo $x->description; ?>"><?php echo $x->name; ?></abbr>
</div>
<?php endforeach; ?>
</div>
</div>
<?php endforeach; ?>
</div>
<input id="show-only-extensions-checkbox" type="checkbox">
<label for="show-only-extensions-checkbox">Only show genes part of enabled extensions</label>
<?php if ($config["gofer2"]["enabled"]): ?>
<p><small>Note: extensions take precedence over other annotations.</small></p>
<?php endif; ?>
</div>
<?php endif; ?>
<div class="accordion-head">
Network
<span style="color:#D84C4F;text-transform:none;font-family:Cambria, Palatino" id="newtrok_mode"></span>
<span style="color:#D84C4F;text-transform:none;font-family:Cambria, Palatino" id="newtrok_mode2"></span>
</div>
<div class="accordion-content">
<label for="pvalueThreshold">Conservation p-value threshold: ≤<span id="pvalueThresholdDisplay">0.05</span></label>
<input id="pvalueThreshold" type="range" min="0" max="0.2" step="0.01" value="0.05">
<div class="network-wrapper">
<div id="cytoscapeweb1" class="network-container">
<div id="network-overlay" class="overlay">
<p class="overlay-message"></p>
<div class="loader_color2 spinner"></div>
</div>
</div>
<div id="annotation-wrapper">
<div id="annotation-toggler"></div>
<div id="annotation-content">
<div id="node-info">
<template id="node-info-template">
<div>
Id: <span></span><br>
Label: <span></span><br>
Parent: <span></span><br>
Coexpression edges: <span></span><br>
Orthology edges: <span></span><br>
</div>
</template>
</div>
<?php if ($config['gofer2']['enabled']): ?>
<div id="annotation-overlay" class="overlay">
<p class="overlay-message"></p>
<div class="loader_color2 spinner"></div>
</div>
<div id="annotation-tabs">
<button class="annotation-tab" value="go">GO</button>
<button class="annotation-tab" value="pfam">PFAM</button>
<button class="annotation-tab" value="kegg">KEGG</button>
</div>
<div id="annotation-control">
<button id="deselect-annotations">Deselect all</button>
<input type="text" id="search-annotation" placeholder="Search...">
</div>
<div id="annotations-list">
<template id="annotation-template">
<div class="annotation-item">
<input type="checkbox">
<div class="label-wrapper">
<label><span class="name"></span><a target="_blank" class="id"></a></label>
</div>
</div>
</template>
</div>
<?php endif; ?>
</div>
</div>
</div>
</div>
<div class="accordion-head">
Tables
<span id="network_info" style="border-radius:5;padding:6px;color:#D84C4F;text-transform:none;font-family:Cambria, Palatino"></span>
</div>
<div class="accordion-content">
<div id="table-tabs">
<template id="table-tab-template">
<button class="table-tab"></button>
</template>
</div>
<div>
<table id="alignement-table" class="stripe nowrap">
<thead>
<tr>
<th>Network</th>
<th></th>
<th>Gene</th>
<th>GO</th>
<th>PFAM</th>
<th>KEGG</th>
</tr>
</thead>
<tbody>
</tbody>
</table>
</div>
</div>
<div class="accordion-head">
Output
</div>
<div class="accordion-content">
Active network:
<span id="active-network"></span>
<textarea id="output-list" class="no-display"></textarea>
<button id="output-copy">Copy to clipboard</button>
<button id="output-save">Save gene list</button>
</div>
<div class="accordion-head">
Citation and Contact us
</div>
<div class="accordion-content ac-extra-medium">
<p>
<strong>A manuscript describing Complex has been published. If you make use of the resource, please cite us:</strong><br>
S. Netotea, D. Sundell, N. R. Street and T. R. Hvidsten. ComPlEx:
conservation and divergence of co-expression networks in A. thaliana,
Populus and O. sativa. BMC Genomics 15:106, 2014.
</p>
</div>
</div>
<div class="lifted_content_box">
© <?php echo date("Y"); ?> UPSC Bioinformatics
</div>
<div id="loader" class="loader_color small"></div>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script>
<script src="lib/jquery.qtip-1.0.0-rc3.min.js"></script>
<script src="https://cdn.datatables.net/v/dt/dt-1.10.16/b-1.5.1/b-colvis-1.5.1/b-html5-1.5.1/r-2.2.1/sl-1.2.5/datatables.min.js"></script>
<script src="https://unpkg.com/cytoscape@3.2.7/dist/cytoscape.min.js"></script>
<script src="https://unpkg.com/webcola@3.4.0/WebCola/cola.js"></script>
<script src="https://unpkg.com/cytoscape-cose-bilkent@1.6.5/cytoscape-cose-bilkent.js"></script>
<script src="https://unpkg.com/cytoscape-cola@2.2.4/cytoscape-cola.js"></script>
<script src="https://unpkg.com/cytoscape-panzoom@2.5.2/cytoscape-panzoom.js"></script>
<script src="https://unpkg.com/cytoscape-cxtmenu@3.0.2/cytoscape-cxtmenu.js"></script>
<!-- <script src="js/fingerprint.js"></script> -->
<script src="js/complexmessage.min.js"></script>
<script src="js/config.js"></script>
<script src="js/networksList.js"></script>
<script src="js/genesLists.js"></script>
<script src="js/alignTrigger.js"></script>
<script src="js/alignmentData.js"></script>
<script src="js/alignmentView.js"></script>
<script src="js/alignmentTable.js"></script>
<script src="js/colorAnnotation.js"></script>
<script src="js/eventLinker.js"></script>
<script src="js/exportManager.js"></script>
<script src="js/extensions.js"></script>
<script src="js/documentation.js"></script>
<script src="js/complex.js"></script>
<script>
//Very cool custom functions
function $_GET(q, s) {
s = s ? s : window.location.search;
var re = new RegExp('&' + q + '(?:=([^&]*))?(?=&|$)', 'i');
return (s = s.replace('?', '&').match(re)) ? (typeof s[1] == 'undefined' ? '' : decodeURIComponent(s[1])) : undefined;
}
if (typeof $_GET('workflow') != 'undefined') {
var workflow="w"+$_GET('workflow');
mannapperuma.startTour(eval(workflow));
}
</script>
</body>
</html>