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browse-all-data.php
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browse-all-data.php
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<?php
require 'dbcon.php';
$sort = $_GET['sort'] ?? '';
$ad = $_GET['ad'] ?? '';
$activity = $_GET['activity'] ?? '';
$target = $_GET['target'] ?? '';
$organism = $_GET['organism'] ?? '';
$exist = $_GET['exist'] ?? '';
$length = $_GET['length'] ?? '';
$finalQuery = array();
$sortFilter = '';
if (strlen($sort) != 0) {
$sortFilter .= 'ORDER BY `' . $sort . '` ' . $ad;
}
$preQuery = '';
$arr = explode(",", $activity);
if (strlen($arr[0]) > 0) {
$preSQLarr = array();
foreach ($arr as $ele) {
array_push($preSQLarr, "`activity` LIKE '%$ele%'");
}
$preQuery .= implode(" AND ", $preSQLarr);
array_push($finalQuery, $preQuery);
}
$preQuery = '';
$arr = explode(",", $target);
if (strlen($arr[0]) > 0) {
$preSQLarr = array();
foreach ($arr as $ele) {
array_push($preSQLarr, "`target organism` LIKE '%$ele%'");
}
$preQuery .= implode(" AND ", $preSQLarr);
array_push($finalQuery, $preQuery);
}
$preQuery = '';
$arr = explode(",", $organism);
if (strlen($arr[0]) > 0) {
$preSQLarr = array();
foreach ($arr as $ele) {
array_push($preSQLarr, "`Organism` LIKE '%$ele%'");
}
$preQuery .= implode(" AND ", $preSQLarr);
array_push($finalQuery, $preQuery);
}
$preQuery = '';
$arr = explode(",", $exist);
if (strlen($arr[0]) > 0) {
$preSQLarr = array();
foreach ($arr as $ele) {
array_push($preSQLarr, "`Protein existence` LIKE '%$ele%'");
}
$preQuery .= implode(" AND ", $preSQLarr);
array_push($finalQuery, $preQuery);
}
$preQuery = '';
$arr = explode(",", $length);
if (strlen($arr[0]) > 0) {
$preQuery .= implode(" AND ", $arr);
array_push($finalQuery, $preQuery);
}
$filterQuery = implode(" AND ", $finalQuery);
if (strlen($filterQuery) > 0) {
$filterQuery = " WHERE " . $filterQuery;
}
?>
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="shortcut icon" href="logo.png" type="image/x-icon">
<title>Browse All Data</title>
<link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.1.3/css/bootstrap.min.css" rel="stylesheet">
<link href="https://cdn.datatables.net/1.13.3/css/dataTables.bootstrap5.min.css" rel="stylesheet">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.4/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.1.3/js/bootstrap.bundle.min.js"></script>
<script src="https://cdn.datatables.net/1.13.3/js/jquery.dataTables.min.js"></script>
<script src="https://cdn.datatables.net/1.13.3/js/dataTables.bootstrap5.min.js"></script>
<link rel="stylesheet" href="ss.css">
<link rel="stylesheet" href="scr.css">
</head>
<body>
<nav class="navbar navbar-expand-sm navbar-dark bg-dark fixed-top">
<div class="container-fluid">
<a class="navbar-brand fs-3" href="ampdb-home">AMPDB v1</a>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#mynavbar">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="mynavbar">
<ul class="navbar-nav me-auto">
<li class="nav-item">
<a class="nav-link" href="ampdb-home">Home</a>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown">Search</a>
<ul class="dropdown-menu">
<li><a class="dropdown-item" href="ampdb-text-search">Text
Search</a></li>
<li><a class="dropdown-item" href="ampdb-specific-search">Specific Text
Search</a></li>
<li><a class="dropdown-item" href="ampdb-target-organism-search">Search by
Target
Organism</a></li>
<li><a class="dropdown-item" href="ampdb-pp-search">Search by
Physicochemical Properties</a>
</li>
<li><a class="dropdown-item" href="ampdb-composition-search">Search by
Protein
Composition</a>
</li>
<li><a class="dropdown-item" href="ampdb-activity-search">Search
by Activity</a></li>
<li><a class="dropdown-item" href="ampdb-advanced-search">Advanced Search</a>
</li>
</ul>
</li>
<li class="nav-item">
<a class="nav-link active" href="browse-all-data">Browse</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-classification">Classification</a>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown">Tools</a>
<ul class="dropdown-menu">
<li><a class="dropdown-item" href="https://ampdb-protein-sequence-alignment-toolbox.streamlit.app/" target="_blank">Protein Sequence Alignment
Toolbox</a></li>
<li><a class="dropdown-item" href="https://ampdb-protein-feature-calculation-toolbox.streamlit.app/" target="_blank">Protein Feature Calculation
Toolbox</a></li>
</ul>
<li class="nav-item">
<a class="nav-link" href="ampdb-data-stat">Statistics</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-downloads">Downloads</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-news">News/Updates</a>
</li>
<li class="nav-item">
<a class="nav-link" href="developers">Developers</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-tutorial">Tutorial</a>
</li>
<li class="nav-item">
<a class="nav-link" href="contact">Contact</a>
</li>
</ul>
<form class="d-flex" action="ampdb-quick-search-result" method="get">
<input name="term" class="form-control me-2" type="text" placeholder="Quick Search">
<input type="submit" value="Search" name="search" class="btn btn-primary">
</form>
</div>
</div>
</nav>
<br><br>
<div class="container-fluid">
<div class="row justify-content-center">
<div class="col-lg-19 bg-light rounded my-2 py-2">
<h4 class="text-center text-success" style="font-size: 500; margin-top: 2%;"> Browse All
Data of AMPDB
(Currently <?php
$sql = "SELECT Serial_No FROM `master2` $filterQuery $sortFilter";
$result = $con->query($sql);
$totRec = mysqli_num_rows($result);
echo $totRec;
?> entries enlisted in AMPDB)
</h4>
<div class="container-fluid">
<div class="row">
<div class="col-sm-6">
<span id="search-term"></span>
</div>
</div>
</div>
</div>
<hr>
</div>
</div>
<div class="container-fluid mt-4">
<div class="row">
<div class="col-sm">
<form id="myForm" method="post" action="request.php">
<div style="margin-left: 5%;">
<button class="btn btn-sm btn-primary" style="margin-top: 1%;" type="button" data-bs-toggle="offcanvas" data-bs-target="#demo">
Filter By
</button>
<button class="btn btn-sm btn-warning " style="margin-top: 1%;" type="button" data-bs-toggle="" data-bs-target="" onclick="toggleCheckboxes(document.querySelectorAll('input[type=checkbox][name=ampdbid]'))">Select
All</button>
<input name="ids" type="text" id="result" style="display: none;">
<input name="allids" type="text" value="<?php
$sort = $_GET['sort'] ?? '';
$ad = $_GET['ad'] ?? '';
$activity = $_GET['activity'] ?? '';
$target = $_GET['target'] ?? '';
$organism = $_GET['organism'] ?? '';
$exist = $_GET['exist'] ?? '';
$length = $_GET['length'] ?? '';
$finalQuery = array();
$sortFilter = '';
if (strlen($sort) != 0) {
$sortFilter .= 'ORDER BY `' . $sort . '` ' . $ad;
}
$preQuery = '';
$arr = explode(",", $activity);
if (strlen($arr[0]) > 0) {
$preSQLarr = array();
foreach ($arr as $ele) {
array_push($preSQLarr, "`activity` LIKE '%$ele%'");
}
$preQuery .= implode(" AND ", $preSQLarr);
array_push($finalQuery, $preQuery);
}
$preQuery = '';
$arr = explode(",", $target);
if (strlen($arr[0]) > 0) {
$preSQLarr = array();
foreach ($arr as $ele) {
array_push($preSQLarr, "`target organism` LIKE '%$ele%'");
}
$preQuery .= implode(" AND ", $preSQLarr);
array_push($finalQuery, $preQuery);
}
$preQuery = '';
$arr = explode(",", $organism);
if (strlen($arr[0]) > 0) {
$preSQLarr = array();
foreach ($arr as $ele) {
array_push($preSQLarr, "`Organism` LIKE '%$ele%'");
}
$preQuery .= implode(" AND ", $preSQLarr);
array_push($finalQuery, $preQuery);
}
$preQuery = '';
$arr = explode(",", $exist);
if (strlen($arr[0]) > 0) {
$preSQLarr = array();
foreach ($arr as $ele) {
array_push($preSQLarr, "`Protein existence` LIKE '%$ele%'");
}
$preQuery .= implode(" AND ", $preSQLarr);
array_push($finalQuery, $preQuery);
}
$preQuery = '';
$arr = explode(",", $length);
if (strlen($arr[0]) > 0) {
$preQuery .= implode(" AND ", $arr);
array_push($finalQuery, $preQuery);
}
$filterQuery = implode(" AND ", $finalQuery);
if (strlen($filterQuery) > 0) {
$filterQuery = " WHERE " . $filterQuery;
}
$sql = "SELECT AMPDB_No_ FROM `master2` $filterQuery $sortFilter";
$result = $con->query($sql);
$myArr = array();
while ($row = $result->fetch_assoc()) {
array_push($myArr, $row['AMPDB_No_']);
}
echo implode(",", $myArr);
?>" style="display: none;">
<input name="ui" class="btn btn-sm btn-success" style="margin-top: 1%;" type="submit" value="Download Selected">
<input name="ui" class="btn btn-sm btn-success" style="margin-top: 1%;" type="submit" value="Download All">
</div>
</form>
</div>
</div>
</div>
<div class="offcanvas offcanvas-start" id="demo">
<div class="offcanvas-header">
<div style="font-weight: 500; font-size: x-large;">Filter Search result</div>
<button type="button" class="btn-close" data-bs-dismiss="offcanvas"></button>
</div>
<div class="offcanvas-body">
<form onsubmit="submitForm(); return false;">
<div>
<button type="submit" class="float-end btn btn-sm btn-success me-2">Apply</button>
<button class="btn btn-sm btn-danger float-end me-1" onclick="removePreChecked()">Clear</button>
<button onclick="uncheckRadios()" type="button" data-bs-toggle="" data-bs-target="" class="btn btn-sm border border-2 float-end me-1" style="background-color: #F0F8FF;">Uncheck
<input class="form-check-input" type="radio" checked></button>
</div>
<br>
<div style="margin-top: 6.5%;">
<?php
$fiLsort = $_GET['sort'] ?? '';
$ad = $_GET['ad'] ?? '';
$fiLactivity = $_GET['activity'] ?? '';
$fiLtarget = $_GET['target'] ?? '';
$fiLorganism = $_GET['organism'] ?? '';
$fiLexist = $_GET['exist'] ?? '';
$fiLlength = $_GET['length'] ?? '';
$finalQuery = array();
$sortFilter = '';
if (strlen($fiLsort) != 0) {
$sortFilter .= 'ORDER BY `' . $fiLsort . '` ' . $ad;
}
$preQuery = '';
$arr = explode(",", $fiLactivity);
if (strlen($arr[0]) > 0) {
$preSQLarr = array();
foreach ($arr as $ele) {
array_push($preSQLarr, "`activity` LIKE '%$ele%'");
}
$preQuery .= implode(" AND ", $preSQLarr);
array_push($finalQuery, $preQuery);
}
$preQuery = '';
$arr = explode(",", $fiLtarget);
if (strlen($arr[0]) > 0) {
$preSQLarr = array();
foreach ($arr as $ele) {
array_push($preSQLarr, "`target organism` LIKE '%$ele%'");
}
$preQuery .= implode(" AND ", $preSQLarr);
array_push($finalQuery, $preQuery);
}
$preQuery = '';
$arr = explode(",", $fiLorganism);
if (strlen($arr[0]) > 0) {
$preSQLarr = array();
foreach ($arr as $ele) {
array_push($preSQLarr, "`Organism` LIKE '%$ele%'");
}
$preQuery .= implode(" AND ", $preSQLarr);
array_push($finalQuery, $preQuery);
}
$preQuery = '';
$arr = explode(",", $fiLexist);
if (strlen($arr[0]) > 0) {
$preSQLarr = array();
foreach ($arr as $ele) {
array_push($preSQLarr, "`Protein existence` LIKE '%$ele%'");
}
$preQuery .= implode(" AND ", $preSQLarr);
array_push($finalQuery, $preQuery);
}
$preQuery = '';
$arr = explode(",", $fiLlength);
if (strlen($arr[0]) > 0) {
$preQuery .= implode(" AND ", $arr);
array_push($finalQuery, $preQuery);
}
$filterQuery = implode(" AND ", $finalQuery);
$forLength = '';
if (strlen($filterQuery) > 0) {
$filterQuery = " WHERE " . $filterQuery;
$forLength = " AND " . implode(" AND ", $finalQuery);
}
$mysort = array("ASC" => "Ascending", "DESC" => "Descending");
$sortArr = array();
foreach ($mysort as $key => $val) {
$match = preg_match_all("/" . str_replace("(", "", str_replace(")", "", str_replace("/", "", $key))) . "/", str_replace("(", "", str_replace(")", "", str_replace("/", "", $ad))));
if ($match != 0) {
$m = '<div class="form-check">
<input type="radio" class="form-check-input" id="' . $key . '" name="ad" value="' . $key . '" checked>
<label style="font-size: smaller;" class="form-check-label" for="' . $key . '">' . $val . '</label>
</div>';
array_push($sortArr, $m);
} else {
$m = '<div class="form-check">
<input type="radio" class="form-check-input" id="' . $key . '" name="ad" value="' . $key . '">
<label style="font-size: smaller;" class="form-check-label" for="' . $key . '">' . $val . '</label>
</div>';
array_push($sortArr, $m);
}
}
?>
<div class="container" style="padding-left:3%;">
<div class="row">
<div class="col-sm" style="padding-left:0px;">
<div class="mb-2" style="font-weight: 500;">Sort Type </div>
<div style="padding-left: 1.7%;">
<?php echo implode("", $sortArr) ?>
</div>
</div>
</div>
</div>
<hr style="height: 3px;">
<?php
$mysort = array("Protein names", "Length", "Gene Names", "Organism", "peptide activity", "target organism");
$sortArr = array();
foreach ($mysort as $thisSort) {
$match = preg_match_all("/" . str_replace("(", "", str_replace(")", "", str_replace("/", "", $thisSort))) . "/", str_replace("(", "", str_replace(")", "", str_replace("/", "", $fiLsort))));
if ($match != 0) {
$m = '<div class="form-check">
<input type="radio" class="form-check-input" id="' . $thisSort . '" name="sort" value="' . $thisSort . '" checked>
<label style="font-size: smaller;" class="form-check-label" for="' . $thisSort . '">' . $thisSort . '</label>
</div>';
array_push($sortArr, $m);
} else {
$m = '<div class="form-check">
<input type="radio" class="form-check-input" id="' . $thisSort . '" name="sort" value="' . $thisSort . '">
<label style="font-size: smaller;" class="form-check-label" for="' . $thisSort . '">' . $thisSort . '</label>
</div>';
array_push($sortArr, $m);
}
}
?>
<div class="container" style="padding-left: 3%;">
<div class="row">
<div class="col-sm" style="padding-left:0px;">
<div class="mb-2" style="font-weight: 500;">Sort By</div>
<div style="padding-left: 1.7%;">
<?php echo implode("", $sortArr) ?>
</div>
</div>
</div>
</div>
<hr style="height: 3px;">
<?php
$sql = "SELECT `peptide activity` FROM `master2` $filterQuery";
$result = $con->query($sql);
$targetArr = array();
while ($row = $result->fetch_assoc()) {
$myTarget = $row['peptide activity'];
array_push($targetArr, $myTarget);
}
$targetArrString = implode(";", $targetArr);
$assocTarget = array();
$targetList = array('Amphibian defense peptide', 'Anti-HSV', 'Anti-MRSA', 'Anti-biofilm', 'Anti-candida', 'Anti-gram-Positive', 'Anti-gram-negative', 'Anti-hepatities', 'Anti-listeria', 'Anti-malarial', 'Anti-mollicute', 'Anti-parasitic', 'Anti-plasmodium', 'Anti-protozoal', 'Anti-tuberculosis', 'Anti-yeast', 'Antibiotic', 'Antimicrobial', 'Antioxidant', 'Antiviral protein', 'Bacteriocin', 'Bacteriolytic enzyme', 'Defensin', 'Fungicide', 'Lantibiotic', 'Plant defense');
foreach ($targetList as $trget) {
$match = preg_match_all("/" . str_replace("(", "", str_replace(")", "", str_replace("/", "", $trget))) . "/", str_replace("/", "", str_replace("(", "", str_replace(")", "", $targetArrString))));
if ($match != 0) {
$assocTarget[$trget] = $match;
}
}
arsort($assocTarget);
$mySelectedAct = array();
foreach ($assocTarget as $key => $val) {
$match = preg_match_all("/" . str_replace("(", "", str_replace(")", "", str_replace("/", "", $key))) . "/", str_replace("(", "", str_replace(")", "", str_replace("/", "", $fiLactivity))));
if ($match != 0) {
$m = '<div class="form-check" style="font-size: smaller"><input type="checkbox" class="form-check-input"
id="' . $key . '" name="activity" value="' . $key . '" checked><label class="form-check-label"
for="' . $key . '" >' . $key . ' (' . $val . ')' . '</label></div>';
array_push($mySelectedAct, $m);
} else {
$m = '<div class="form-check" style="font-size: smaller"><input type="checkbox" class="form-check-input"
id="' . $key . '" name="activity" value="' . $key . '"><label class="form-check-label"
for="' . $key . '" >' . $key . ' (' . $val . ')' . '</label></div>';
array_push($mySelectedAct, $m);
}
}
?>
<div class="continer ">
<div class="row">
<div class="col-sm">
<div class="mb-2" style="font-weight: 500;">Antimicrobial Activity</div>
<?php if (count($mySelectedAct) > 10) { ?>
<div class="scr" style="padding-left: 1.7%; padding-top:0.5%; padding-bottom: 0.5%;">
<?php echo (implode("", $mySelectedAct)); ?>
</div>
<?php } else { ?>
<div style="padding-left: 1.7%; padding-top:0.5%; padding-bottom: 0.5%;">
<?php echo (implode("", $mySelectedAct)); ?>
</div>
<?php } ?>
</div>
</div>
</div>
<hr style="height: 3px;">
<?php
$sql = "SELECT `target organism` FROM `master2` $filterQuery";
$result = $con->query($sql);
$targetArr = array();
while ($row = $result->fetch_assoc()) {
$myTarget = $row['target organism'];
if ($myTarget != 'No Target Organism Found') {
array_push($targetArr, $myTarget);
}
}
$targetArrString = implode(";", $targetArr);
$assocTarget = array();
$targetList = array('A.actinomycetemcomitans (Gram-negative)', 'A.alternata', 'A.baumannii (Gram-negative)', 'A.benhamiae', 'A.brassicae', 'A.brassicicola', 'A.calcoaceticus (Gram-negative)', 'A.cucumerina', 'A.domesticus', 'A.faecalis (Gram-positive)', 'A.flavus (Not characterize)', 'A.fumigatus', 'A.globiformis (Gram-positive)', 'A.hydrophila (Gram-negative)', 'A.laidlawii (Gram-positive)', 'A.lycopersici', 'A.nidulans (Gram-positive)', 'A.niger', 'A.parasiticus', 'A.pisum', 'A.salmonicida (Gram-negative)', 'A.solani', 'A.stephensi', 'A.terreus (Not characterize)', 'A.tumefaciens (Gram-negative)', 'A.viridans (Gram-positive)', 'A.viscosus (Gram-positive)', 'Acinetobacter baumannii (Gram-negative)', 'Acinetobacter spec. (Gram-negative)', 'Actinomyces (Gram-positive)', 'Acute', 'Aeropyrum pernix', 'African green', 'Alternaria solani', 'Aspergillus oryzae', 'Aspergillus terreus', 'B.adolescentis (Gram-positive)', 'B.algicola (Not characterize)', 'B.amyloliquefaciens (Gram-positive)', 'B.anthracis (Gram-positive)', 'B.bacteriovorus (Gram-negative)', 'B.bassiana', 'B.breve (Gram-positive)', 'B.brevis (Gram-positive)', 'B.cepacia (Gram-negative)', 'B.cereus (Gram-positive)', 'B.cinerea', 'B.coagulans (Gram-positive)', 'B.dendrobatidis', 'B.licheniformis (Gram-positive)', 'B.longum (Gram-positive)', 'B.magaterium (Gram-positive)', 'B.malayi', 'B.megaterium', 'B.mycoides (Gram-positive)', 'B.pertussis (Gram-negative)', 'B.pumilus (Gram-positive)', 'B.sorokiniana', 'B.subtilis (Gram-positive)', 'B.thuringiensis (Gram-positive)', 'Bacillus (Gram-positive)', 'Bacillus cereus (Gram-positive)', 'Bacillus megaterium (Gram-positive)', 'Bacillus subtilis (Gram-positive)', 'Beauveria', 'Burkholderia (Gram-negative)', 'Burkholderia cepacia (Gram-negative)', 'C.albicans', 'C.albidus', 'C.bovis (Gram-positive)', 'C.cassicola', 'C.coccodes', 'C.comatus', 'C.crenatum (Gram-positive)', 'C.diphtheriae (Gram-positive)', 'C.divergens (Gram-positive)', 'C.freundii (Gram-negative)', 'C.fructus', 'C.glabrata', 'C.globosum', 'C.gloeosporioides', 'C.glutamicum (Gram-positive)', 'C.guilliermondii', 'C.irritans', 'C.jejuni (Gram-negative)', 'C.michiganensis (Gram-positive)', 'C.neoformans', 'C.parapsilosis', 'C.perfringens (Gram-positive)', 'C.sakazakii (Gram-negative)', 'C.sphaerospermum', 'C.sporogenes (Gram-negative)', 'C.tropicalis (Gram-negative)', 'C.versicolor', 'C.wickerhamii', 'Campylobacter (Gram-negative)', 'Candida', 'Candida albicans', 'Candida species', 'Candida spp.', 'Carnobacterium (Gram-positive)', 'Chandipura', 'Clostridium (Gram-positive)', 'Clostridium difficile (Gram-positive)', 'Clostridium spp. (Gram-positive)', 'Collectotrichum', 'Coral', 'Corynebacterium (Gram-positive)', 'Cryptococcus neoformans', 'D.bryoniae', 'D.coniospora', 'D.melanogaster', 'Dengue', 'Drosophila', 'E.Coli (Gram-negative)', 'E.casseliflavus (Gram-positive)', 'E.cloacae (Gram-negative)', 'E.coli (Gram-negative)', 'E.faecalis (Gram-positive)', 'E.faecium (Gram-positive)', 'E.hirae (Gram-positive)', 'Enterobacter (Gram-negative)', 'Enterobacteriaceae (Gram-negative)', 'Enterococcus (Gram-positive)', 'Enterococcus faecalis (Gram-positive)', 'Enterococcus faecium (Gram-positive)', 'Enterococcus sp. (Gram-positive)', 'Epinephelus fario', 'Escherichia coli (Gram-negative)', 'F.avenaceum', 'F.culmorum', 'F.graminearum', 'F.oxysporum', 'F.solani (Gram-positive)', 'F.verticillioides', 'Francisella tularensis (Gram-negative)', 'Fungi', 'Fusarium', 'G.candidum', 'G.trabeum', 'G.vaginalis (Gram-positive)', 'Gram Negative Bacteria', 'Gram Negative Bacteria and Gram Positive Bacteria', 'Gram Positive Bacteria', 'H.annosum', 'H.armigera', 'H.contortus', 'H.influenzae (Gram-negative)', 'H.pylori (Gram-negative)', 'H.rufa', 'Haemophilus influenzae (Gram-negative)', 'Halobacterium', 'Hepatitis B', 'K.oxytoca (Gram-negative)', 'K.pneumonia', 'K.pneumoniae (Gram-negative)', 'K.thermotolerans', 'K.varians (Gram-positive)', 'Klebsiella (Gram-negative)', 'Klebsiella pneumonia (Gram-negative)', 'Klebsiella sp (Gram-negative)', 'Kocuria (Gram-positive)', 'L.acidophilus (Gram-positive)', 'L.amazonensis', 'L.brevis (Gram-positive)', 'L.caesar', 'L.casei (Gram-positive)', 'L.cuprina', 'L.curvatus (Gram-positive)', 'L.fermentum (Gram-positive)', 'L.garvieae (Gram-positive)', 'L.gaucho', 'L.grayi (Gram-positive)', 'L.infantum', 'L.innocua (Gram-positive)', 'L.ivanovii (Gram-positive)', 'L.jensenii (Gram-positive)', 'L.lactis (Gram-positive)', 'L.lindneri', 'L.major', 'L.mesenteroides (Gram-positive)', 'L.monocytogenes (Gram-positive)', 'L.mucor (Gram-negative)', 'L.paracasei (Gram-positive)', 'L.pentosus (Gram-positive)', 'L.plantarum (Gram-positive)', 'L.pneumophila (Gram-negative)', 'L.rhamnosus (Gram-positive)', 'L.sakei (Gram-positive)', 'L.salivarius (Gram-positive)', 'L.seeligeri (Gram-positive)', 'L.viridescens', 'L.welshimeri (Gram-positive)', 'Lactobacillus (Gram-positive)', 'Lactobacillus sakei (Gram-positive)', 'Lactococcus (Gram-positive)', 'Leishmania', 'Leishmania amazonensis', 'Leishmania infantum', 'Leishmania sp.', 'Leishmania species', 'Lepidopteran', 'Leuconostoc (Gram-positive)', 'Leuconostoc mesenteroides (Gram-positive)', 'Listeria (Gram-positive)', 'Listeria monocytogenes (Gram-positive)', 'Listeria spp. (Gram-positive)', 'M.catarrhalis (Gram-negative)', 'M.flavus (Not characterize)', 'M.fortuitum (Gram-positive)', 'M.furfur', 'M.grisea (Gram-positive)', 'M.luteus (Gram-negative)', 'M.maritypicum (Not characterize)', 'M.massiliense (Gram-positive/Gram-negative)', 'M.morganii (Gram-negative)', 'M.nematophilum (Not characterize)', 'M.phlei (Gram-positive)', 'M.rileyi', 'M.smegmatis (Gram-positive)', 'M.tuberculosis (Gram-positive)', 'Micrococcus (Gram-positive)', 'Micrococcus luteus (Gram-positive)', 'Mycobacterium (Gram-positive)', 'Mycobacterium abscessus (Gram-positive)', 'Mycobacterium bovis (Gram-positive)', 'Mycobacterium species (Gram-positive)', 'Mycobacterium tuberculosis (Gram-positive)', 'Mycoplasma (Gram-negative)', 'N.cinerea (Gram-negative)', 'N.crassa', 'N.gonorrhoeae (Gram-negative)', 'Neurospora', 'Neurospora crassa', 'P.acidilactici (Gram-positive)', 'P.acnes', 'P.aeruginosa (Gram-negative)', 'P.alginovora (Gram-negative)', 'P.berghei', 'P.beta', 'P.betae', 'P.brasiliensis (Gram-positive/Gram-negative)', 'P.capsici (Gram-negative)', 'P.chrysosporium', 'P.denitrificans (Gram-negative)', 'P.digitatum', 'P.entomophila (Gram-negative)', 'P.falciparum', 'P.fluorescens (Gram-negative)', 'P.freudenreichii (Gram-positive)', 'P.granivorans (Gram-positive)', 'P.haemolytica (Gram-negative)', 'P.immobilis (Gram-negative)', 'P.infestans', 'P.jensenii', 'P.larvae (Gram-positive)', 'P.meadii', 'P.micros', 'P.mirabilis (Gram-negative)', 'P.multocida (Gram-negative)', 'P.nicotianae (Gram-positive)', 'P.pastoris', 'P.paucidens', 'P.pentosaceus (Gram-positive)', 'P.piricola', 'P.placenta', 'P.putida (Gram-negative)', 'P.rettgeri (Gram-negative)', 'P.rhodesiae (Gram-negative)', 'P.syringae (Gram-negative)', 'P.tannophilus', 'P.ultimum', 'P.verrucosum', 'P.versicolor (Gram-negative)', 'P.vulgaris (Gram-negative)', 'P.wickerhamii', 'Pediococcus (Gram-positive)', 'Penicillium digitatum', 'Plasmodium berghei', 'Plasmodium gallinaceum', 'Propionibacterium (Gram-positive)', 'Proteus (Gram-negative)', 'Pseudomonas (Gram-negative)', 'Pseudomonas aeruginosa (Gram-negative)', 'Pseudomonas sp. (Gram-negative)', 'R.cerealis', 'R.equi', 'R.mucilaginosa (Gram-positive)', 'R.rhodochrous (Gram-positive)', 'R.solani', 'R.stolonifer', 'Rhizomucor pusillus', 'Rhodococcus sp. (Gram-positive)', 'S.agalactiae (Gram-positive)', 'S.aureus (Gram-positive)', 'S.bovis (Gram-negative)', 'S.boydii (Gram-negative)', 'S.carnaria', 'S.carnosus (Gram-positive)', 'S.cerevisiae', 'S.choleraesuis', 'S.commune', 'S.dysenteriae (Gram-negative)', 'S.dysgalactiae (Gram-positive)', 'S.enterica (Gram-negative)', 'S.enteritidis', 'S.epidermidis (Gram-positive)', 'S.epidermis', 'S.equi (Gram-positive)', 'S.faecalis (Gram-positive)', 'S.flexneri (Gram-negative)', 'S.frugiperda', 'S.gallinarum (Gram-positive)', 'S.haemolyticus (Gram-positive)', 'S.hemolyticus', 'S.hominis (Gram-negative)', 'S.iniae (Gram-positive)', 'S.lutea (Gram-negative)', 'S.mansoni', 'S.marcescens (Gram-negative)', 'S.melliferum (Gram-positive)', 'S.mutans (Gram-positive)', 'S.pneumoniae (Gram-positive)', 'S.pombe', 'S.pyogenes (Gram-positive)', 'S.saprophyticus (Gram-positive)', 'S.sclerotiorum', 'S.sonnei (Gram-negative)', 'S.suis (Gram-positive)', 'S.thermophilus (Gram-positive)', 'S.typhi', 'S.typhimurium', 'S.uberis (Gram-positive)', 'S.warneri (Gram-positive)', 'S.xylosus (Gram-positive)', 'Salmonella (Gram-negative)', 'Salmonella sp. (Gram-negative)', 'Salmonella species (Gram-negative)', 'Serratia marcescens (Gram-negative)', 'Shigella (Gram-negative)', 'Staphylococcus (Gram-positive)', 'Staphylococcus aureus (Gram-positive)', 'Staphylococcus species (Gram-positive)', 'Staphylococcus spp. (Gram-positive)', 'Streptococcus (Gram-positive)', 'Streptococcus sp. (Gram-positive)', 'Streptococcus uberis (Gram-positive)', 'T.beigelii', 'T.brucei', 'T.cruzi', 'T.delbrueckii', 'T.denticola (Gram-negative)', 'T.gondii', 'T.harzianum', 'T.reesei', 'T.viride', 'Tick', 'Toxoplasma gondii', 'Trichoderma', 'Trichoderma reesei', 'Trichoderma species', 'Trichophyton rubrum', 'Trichosporon spp.', 'Trypanosoma', 'Trypanosoma cruzi', 'V.alginolyticus (Gram-negative)', 'V.anguillarum (Gram-negative)', 'V.cholerae (Gram-negative)', 'V.dahliae', 'V.fluvialis (Gram-positive)', 'V.harveyi (Gram-negative)', 'V.parahaemolyticus (Gram-negative)', 'V.penaeicida (Gram-negative)', 'V.vulnificus (Gram-negative)', 'Vibrio (Gram-negative)', 'X.axonopodis (Gram-negative)', 'X.campestris (Gram-negative)', 'Xanthomonas axonopodis (Gram-negative)', 'Y.enterocolitica (Gram-negative)', 'Y.pseudotuberculosis (Gram-negative)', 'Yellow Fever', 'Yersinia (Gram-negative)', 's.marcescens (Gram-negative)');
foreach ($targetList as $trget) {
$match = preg_match_all("/" . str_replace(")", "", str_replace("(", "", str_replace("/", "", $trget))) . "/", str_replace("/", "", str_replace(")", "", str_replace("(", "", $targetArrString))));
if ($match != 0) {
$assocTarget[$trget] = $match;
}
}
arsort($assocTarget);
$mySelectedAct = array();
foreach ($assocTarget as $key => $val) {
$match = preg_match_all("/" . str_replace("(", "", str_replace(")", "", str_replace("/", "", $key))) . "/", str_replace("(", "", str_replace(")", "", str_replace("/", "", $fiLtarget))));
if ($match != 0) {
$m = '<div class="form-check" style="font-size: smaller"><input type="checkbox" class="form-check-input"
id="' . $key . '" name="target" value="' . $key . '" checked><label class="form-check-label"
for="' . $key . '" >' . $key . ' (' . $val . ')' . '</label></div>';
array_push($mySelectedAct, $m);
} else {
$m = '<div class="form-check" style="font-size: smaller"><input type="checkbox" class="form-check-input"
id="' . $key . '" name="target" value="' . $key . '"><label class="form-check-label"
for="' . $key . '" >' . $key . ' (' . $val . ')' . '</label></div>';
array_push($mySelectedAct, $m);
}
}
?>
<div class="continer ">
<div class="row">
<div class="col-sm">
<div class="mb-2" style="font-weight: 500;">Target Organism</div>
<?php if (count($mySelectedAct) > 10) { ?>
<div class="scr" style="padding-left: 1.7%; padding-top:0.5%; padding-bottom: 0.5%;">
<?php echo (implode("", $mySelectedAct)); ?>
</div>
<?php } else { ?>
<div style="padding-left: 1.7%; padding-top:0.5%; padding-bottom: 0.5%;">
<?php echo (implode("", $mySelectedAct)); ?>
</div>
<?php } ?>
</div>
</div>
</div>
<hr style="height: 3px;">
<?php
$sql = "SELECT `Organism` FROM `master2` $filterQuery";
$result = $con->query($sql);
$targetArr = array();
while ($row = $result->fetch_assoc()) {
$myTarget = $row['Organism'];
array_push($targetArr, explode("(", $myTarget)[0]);
}
$targetArrString = implode(" ", $targetArr);
$mysql = "SELECT DISTINCT(`Organism`) FROM `master2` $filterQuery";
$targetList = array();
$myResult = $con->query($mysql);
while ($row = $myResult->fetch_assoc()) {
array_push($targetList, explode("(", $row['Organism'])[0]);
}
$assocTarget = array();
$c = 1;
foreach ($targetList as $trget) {
$match = preg_match_all("/" . str_replace("(", "", str_replace(")", "", str_replace("/", "", $trget))) . "/", str_replace("(", "", str_replace(")", "", str_replace("/", "", $targetArrString))));
if ($match > 1) {
$assocTarget[$trget] = $match;
}
if ($c == 50) {
break;
}
$c += 1;
$targetArrString = str_replace("$trget", "", $targetArrString);
}
arsort($assocTarget);
$mySelectedAct = array();
foreach ($assocTarget as $key => $val) {
$match = preg_match_all("/" . str_replace("(", "", str_replace(")", "", str_replace("/", "", $key))) . "/", str_replace("(", "", str_replace(")", "", str_replace("/", "", $fiLorganism))));
if ($match != 0) {
$m = '<div class="form-check" style="font-size: smaller"><input type="checkbox" class="form-check-input"
id="' . $key . '" name="organism" value="' . $key . '" checked><label class="form-check-label"
for="' . $key . '" >' . $key . ' (' . $val . ')' . '</label></div>';
array_push($mySelectedAct, $m);
} else {
$m = '<div class="form-check" style="font-size: smaller"><input type="checkbox" class="form-check-input"
id="' . $key . '" name="organism" value="' . $key . '"><label class="form-check-label"
for="' . $key . '" >' . $key . ' (' . $val . ')' . '</label></div>';
array_push($mySelectedAct, $m);
}
}
?>
<div class="continer ">
<div class="row">
<div class="col-sm">
<div class="mb-2" style="font-weight: 500;">Common Source Organism</div>
<?php if (count($mySelectedAct) > 10) { ?>
<div class="scr" style="padding-left: 1.7%; padding-top:0.5%; padding-bottom: 0.5%;">
<?php echo (implode("", $mySelectedAct)); ?>
</div>
<?php } else { ?>
<div style="padding-left: 1.7%; padding-top:0.5%; padding-bottom: 0.5%;">
<?php echo (implode("", $mySelectedAct)); ?>
</div>
<?php } ?>
</div>
</div>
</div>
<hr style="height: 3px;">
<?php
$sql = "SELECT `Protein existence` FROM `master2` $filterQuery";
$result = $con->query($sql);
$targetArr = array();
while ($row = $result->fetch_assoc()) {
$myTarget = $row['Protein existence'];
array_push($targetArr, $myTarget);
}
$targetArrString = implode(";", $targetArr);
$assocTarget = array();
$targetList = array('Predicted', 'Homology', 'Transcript level', 'Protein level', 'Uncertain');
foreach ($targetList as $trget) {
$match = preg_match_all("/" . str_replace("(", "", str_replace(")", "", str_replace("/", "", $trget))) . "/i", str_replace("(", "", str_replace(")", "", str_replace("/", "", $targetArrString))));
if ($match != 0) {
$assocTarget[$trget] = $match;
}
}
arsort($assocTarget);
$mySelectedAct = array();
foreach ($assocTarget as $key => $val) {
$match = preg_match_all("/" . str_replace("(", "", str_replace(")", "", str_replace("/", "", $key))) . "/", str_replace("(", "", str_replace(")", "", str_replace("/", "", $fiLexist))));
if ($match != 0) {
$m = '<div class="form-check" style="font-size: smaller"><input type="checkbox" class="form-check-input"
id="' . $key . '" name="exist" value="' . $key . '" checked><label class="form-check-label"
for="' . $key . '" >' . $key . ' (' . $val . ')' . '</label></div>';
array_push($mySelectedAct, $m);
} else {
$m = '<div class="form-check" style="font-size: smaller"><input type="checkbox" class="form-check-input"
id="' . $key . '" name="exist" value="' . $key . '"><label class="form-check-label"
for="' . $key . '" >' . $key . ' (' . $val . ')' . '</label></div>';
array_push($mySelectedAct, $m);
}
}
?>
<div class="continer ">
<div class="row">
<div class="col-sm">
<div class="mb-2" style="font-weight: 500;">Protein Existence Level</div>
<div style="padding-left: 1.7%; padding-top:0.5%; padding-bottom: 0.5%;">
<?php echo (implode("", $mySelectedAct)); ?>
</div>
</div>
</div>
</div>
<hr style="height: 3px;">
<?php
$mySelectedAct = array();
$start = 1;
$end = 100;
$assArr = array();
for ($i = 0; $i < 6; $i += 1) {
$myval = '';
if ($start > 500) {
$myval = " Length > 500 ";
} else {
$myval = " Length BETWEEN $start AND $end ";
}
$mysql5 = "SELECT COUNT(Serial_No) FROM `master2` WHERE $myval $forLength";
$assOxx = $con->query($mysql5);
$mydata = $assOxx->fetch_all()[0][0];
if ($mydata > 0) {
$assArr[$myval] = $mydata;
}
$start += 100;
$end += 100;
}
foreach ($assArr as $key => $val) {
$match = preg_match_all("/" . str_replace("(", "", str_replace(")", "", str_replace("/", "", $key))) . "/", str_replace("(", "", str_replace(")", "", str_replace("/", "", $fiLlength))));
if ($match != 0) {
$m = '<div class="form-check">
<input type="radio" class="form-check-input" id="' . $key . '" name="length" value="' . $key . '" checked>
<label style="font-size: smaller;" class="form-check-label" for="' . $key . '">' . str_replace('AND', 'TO', str_replace(' Length ', '', str_replace(' Length BETWEEN ', '', $key))) . ' (' . $val . ')' . '</label>
</div>';
array_push($mySelectedAct, $m);
} else {
$m = '<div class="form-check">
<input type="radio" class="form-check-input" id="' . $key . '" name="length" value="' . $key . '">
<label style="font-size: smaller;" class="form-check-label" for="' . $key . '">' . str_replace('AND', 'TO', str_replace(' Length ', '', str_replace(' Length BETWEEN ', '', $key))) . ' (' . $val . ')' . '</label>
</div>';
array_push($mySelectedAct, $m);
}
}
?>
<div class="continer ">
<div class="row">
<div class="col-sm">
<div class="mb-2" style="font-weight: 500;">Sequence Length</div>
<div style="padding-left: 1.7%; padding-top:0.5%; padding-bottom: 0.5%;">
<?php
echo (implode("", $mySelectedAct));
$con->close();
?>
</div>
</div>
</div>
</div>
</div>
</form>
</div>
</div>
<div class="container-fluid" id="data" style="width: 90%;">
</div>
<div class="container d-flex justify-content-center">
<div class="spinner-border m-5 text-success" id="loading" role="status">
<span class="visually-hidden">Loading...</span>
</div>
</div>
<script>
function uncheckRadios() {
var radioButtons = document.querySelectorAll('input[type="radio"]');
radioButtons.forEach(function(radio) {
radio.checked = false;
});
}
function removePreChecked() {
var radioButtons = document.querySelectorAll('input[type="radio"]');
var checkboxes = document.querySelectorAll('input[type="checkbox"]');
radioButtons.forEach(function(radio) {
radio.checked = false;
});
checkboxes.forEach(function(checkbox) {
checkbox.checked = false;
});
}
function updateTextbox(checkbox) {
var resultTextbox = document.getElementById("result");
var checkboxValue = checkbox.value;
if (checkbox.checked) {
if (resultTextbox.value === '') {
resultTextbox.value += checkboxValue;
} else {
resultTextbox.value += ',' + checkboxValue;
}
} else {
var currentValue = resultTextbox.value;
var newValue = currentValue
.replace(checkboxValue + ',', '')
.replace(',' + checkboxValue, '')
.replace(checkboxValue, '');
resultTextbox.value = newValue;
}
}
function uncheckCheckbox() {
var checkbox = document.querySelector('input[name="sort"]');
checkbox.checked = false;
}
function toggleCheckboxes() {
const checkboxes = document.querySelectorAll('input[type=checkbox][name=ampdbid]');
const isChecked = checkboxes[0].checked;
const checkedValues = [];
for (let i = 0; i < checkboxes.length; i++) {
checkboxes[i].checked = !isChecked;
if (checkboxes[i].checked) {
checkedValues.push(checkboxes[i].value);
}
}
const resultInput = document.getElementById('result');
resultInput.value = checkedValues.join(',');
}
function getAllParameterValues(parameterName) {
var url = window.location.href;
var queryString = url.substring(url.indexOf('?') + 1);
var parameterPairs = queryString.split('&');
var parameterValues = [];
for (var i = 0; i < parameterPairs.length; i++) {
var pair = parameterPairs[i].split('=');
var name = decodeURIComponent(pair[0]);
var value = decodeURIComponent(pair[1]);
if (name === parameterName) {
parameterValues.push(value);
}
}
return parameterValues.join(",").replace(/\+/g, " ");
}
const activity = getAllParameterValues('activity');
const target = getAllParameterValues('target');
const organism = getAllParameterValues('organism');
const exist = getAllParameterValues('exist');
const len = getAllParameterValues('length');
const sort = getAllParameterValues('sort')
const ad = getAllParameterValues('ad');
var myR = <?php echo $totRec; ?>;
$(window).scroll(function() {
if (myR > -1) {
if ($(window).scrollTop() + $(window).height() > $(document).height() - 220) {
if (!isrunning) {
showdata();
myR -= 10;
}
}
}
});
var page_no = 1;
var isrunning = false;
showdata();
function showdata() {
isrunning = true;
$("#loading").show();
$.post("data-browse-all-data.php", {
page: page_no,
activity: activity,
target: target,
organism: organism,
exist: exist,
length: len,
sort: sort,
ad: ad
}, (response) => {
$("#data").append(response);
$("#loading").hide();
isrunning = false;
page_no++;
});
}
function submitForm() {
const checkboxes1 = document.querySelectorAll('input[type="checkbox"][name="activity"]:checked');
const values1 = [];
checkboxes1.forEach((checkbox) => {
values1.push(checkbox.value);
});
const urlParams1 = new URLSearchParams(window.location.search);
urlParams1.set('activity', values1.join(','));
const checkboxes2 = document.querySelectorAll('input[type="checkbox"][name="target"]:checked');
const values2 = [];
checkboxes2.forEach((checkbox) => {
values2.push(checkbox.value);
});
const urlParams2 = new URLSearchParams(window.location.search);
urlParams2.set('target', values2.join(','));
const checkboxes3 = document.querySelectorAll('input[type="checkbox"][name="organism"]:checked');
const values3 = [];
checkboxes3.forEach((checkbox) => {
values3.push(checkbox.value);
});
const urlParams3 = new URLSearchParams(window.location.search);
urlParams3.set('organism', values3.join(','));
const checkboxes4 = document.querySelectorAll('input[type="checkbox"][name="exist"]:checked');
const values4 = [];
checkboxes4.forEach((checkbox) => {
values4.push(checkbox.value);
});
const urlParams4 = new URLSearchParams(window.location.search);
urlParams4.set('exist', values4.join(','));
const checkboxes5 = document.querySelectorAll('input[type="radio"][name="length"]:checked');
const values5 = [];
checkboxes5.forEach((checkbox) => {
values5.push(checkbox.value);
});
const urlParams5 = new URLSearchParams(window.location.search);
urlParams5.set('length', values5.join(','));
const radioButton = document.querySelector('input[type="radio"][name="sort"]:checked');
const value2 = radioButton ? radioButton.value : '';
const urlParams6 = new URLSearchParams(window.location.search);
urlParams6.set('sort', value2);
const radioButton7 = document.querySelector('input[type="radio"][name="ad"]:checked');
const value7 = radioButton7 ? radioButton7.value : '';
const urlParams7 = new URLSearchParams(window.location.search);
urlParams7.set('ad', value7);
window.location.href = new 'browse-all-data?' + urlParams1.toString() + '&' + urlParams2.toString() + '&' + urlParams3.toString() + '&' + urlParams4.toString() + '&' + urlParams5.toString() + '&' + urlParams6.toString() + '&' + urlParams7.toString();
}
</script>
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</body>
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