-
Notifications
You must be signed in to change notification settings - Fork 2
/
index.php
executable file
·98 lines (92 loc) · 4.11 KB
/
index.php
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
<?php if(!isset($_SESSION)){session_start();} ?>
<?php if(!isset($_SESSION["db_ids"])){$_SESSION["db_ids"]=array();} ?>
<?php if(!isset($_SESSION["blast_ids"])){$_SESSION["blast_ids"]=array();} ?>
<!DOCTYPE HTML>
<html>
<?php
require_once('lib_db.php');
require_once('common.php');
?>
<head>
<meta charset="UTF-8">
<title><?php site_name(); ?> tools</title>
<link rel="icon" type="image/png" href="css/Synteruptor_logo_square.png">
<link rel="stylesheet" type="text/css" href="css/common.css">
<link rel="stylesheet" type="text/css" href="css/index.css">
<script type="text/javascript" src="js/jquery/jquery-1.12.min.js"></script>
<script type="text/javascript" src="js/common.js"></script>
<script type="text/javascript" src="js/index.js"></script>
</head>
<nav><?php print_sidebar(); ?></nav>
<body>
<?php print_header(); ?>
<div id="content">
<div class="centered_box">
<div id="site_description">
<div class='index_box'>
<!--<img src='css/Synteruptor_logo_full.png' id='logo' alt='logo' />-->
<h2>About <?php echo $site_name ?></h2>
<p><?php echo $site_name ?> is a tool designed to find synteny breaks between closely related bacterial genomes. The breaks found can be explored with this web interface to find clusters of genes of interest.</p>
<br /><span id="last_update">Last update: <?php echo get_setting("last_update"); ?></span>
<br /><span id="contact">Contact: <?php echo get_mail(); ?></span>
<span style="float:right;"><a href="download.php">Download <?php echo $site_name ?></a></span>
<div style='clear:both;'></div>
</div>
<div class="index_box">
<h2>How to use the <?php echo $site_name ?> website</h2>
<p>Synteruptor can be used in several ways:
<ul>
<li>either explore a precomputed, available database: <a href="explore_db.php">Explore databases</a></li>
<li>or create your own database with your own genome files: <a href="createdb.php">Create database</a>. The created database will be private, but it can be explored like any of the precomputed database</li>
</ul>
</p>
<p>You can also:
<ul>
<li>Search individual sequences within your or precomputed databases: <a href="search.php">Search databases</a></li>
<li>or directly access previously identified genomic islands: <a href="direct_access.php">Genomic islands</a></li>
</ul>
</p>
</div>
<!--
<div class='index_box'>
<h2>How to use the <?php echo $site_name ?> website</h2>
//<p>Synteruptor can be used in several ways:<ul>
// <li>either explore a precomputed, available database</li>
// <li>or create your own database with your own genome files. The created database will be private, but it can be explored like any of the precomputed database</li>
//</ul>
//</p>
<?php
// Display public databases (if any)
echo "<h3 id='availdb'>Available databases</h3>";
$allowed = get_available_dbs_list();
if ($allowed) {
echo "<p>The following databases were generated with preselected genomes and can be freely explored:</p>";
echo "<div id='databases'></div>";
} else {
echo "<p>No public database available</p>";
}
// Direct access to the genomic islands
echo "<h3>Direct access to the genomic islands</h3>";
if ($allowed) {
echo "<p>The genomic islands identified in the previous databases can be directly accessed with their identifier:</p>";
echo "<div class='button_container'><a href='direct_access.php'><div class='button_link'>Access to a genomic island</div></a></div>";
echo "<div id='databases'></div>";
} else {
echo "<p>No public database available</p>";
}
// Show database creator link if active
echo "<h3>Database creation</h3>";
if (get_setting("can_upload")) {
echo "<p>Upload your genomes to create a $site_name database:</p>";
echo "<div class='button_container'><a href='createdb.php'><div class='button_link'>Create a $site_name database</div></a></div>";
} else {
echo "<p>Database creation is not activated on this website</p>";
}
?>
</div> -->
</div>
</div>
</div>
<?php print_footer();?>
</body>
</html>