-
Notifications
You must be signed in to change notification settings - Fork 1
/
results.php
270 lines (256 loc) · 11.2 KB
/
results.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
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
<?php
include_once('common.php');
include_once('partials/header.php');
?>
<div class="container">
<div class="row">
<div class="col-md-8 col-md-offset-2">
<?php include_once('partials/search.php'); ?>
</div>
</div>
<div class="row">
<div class="col-md-10 col-md-offset-1">
<h4><strong>Summary</strong></h4><hr>
<div class="jumbotron">
<?php
$q = $_GET['q'];
$sp = isset($_GET['species']) ? $_GET['species'] : '';
$gr = isset($_GET['group']) ? $_GET['group'] : '';
$page = isset($_GET['page']) ? $_GET['page'] : '1';
$s = isset($_GET['page']) ? (($_GET['page'] - 1) * 10) : '0';
$query = "SELECT COUNT(*) FROM proteins WHERE
(`Protein_Name` LIKE ? OR `Domain_Group` LIKE ? OR `Uniprot_ID` LIKE ?)
AND `Species` LIKE ? AND `Domain_Group` LIKE ?";
$stmt = $dbh->prepare($query);
$param = array("%$q%", "%$q%", "%$q%", "%$sp%", "%$gr%");
$stmt->execute($param);
$total = $stmt->fetch()[0];
$total_pages = ceil($total / 10);
$query = "SELECT COUNT(DISTINCT `Uniprot_ID`) FROM proteins WHERE
(`Protein_Name` LIKE ? OR `Domain_Group` LIKE ? OR `Uniprot_ID` LIKE ?)
AND `Species` LIKE ? AND `Domain_Group` LIKE ?";
$stmt = $dbh->prepare($query);
$stmt->execute($param);
$total_proteins = $stmt->fetch()[0];
$query = "SELECT COUNT(DISTINCT `Protein_Name`) FROM proteins WHERE
(`Protein_Name` LIKE ? OR `Domain_Group` LIKE ? OR `Uniprot_ID` LIKE ?)
AND `Species` LIKE ? AND `Domain_Group` LIKE ?";
$stmt = $dbh->prepare($query);
$stmt->execute($param);
$total_pwms = $stmt->fetch()[0];
$query = "SELECT COUNT(DISTINCT `Domain_Group`) FROM proteins WHERE
(`Protein_Name` LIKE ? OR `Domain_Group` LIKE ? OR `Uniprot_ID` LIKE ?)
AND `Species` LIKE ? AND `Domain_Group` LIKE ?";
$stmt = $dbh->prepare($query);
$stmt->execute($param);
$total_families = $stmt->fetch()[0];
$query = "SELECT * FROM proteins WHERE
(`Protein_Name` LIKE ? OR `Domain_Group` LIKE ? OR `Uniprot_ID` LIKE ?)
AND `Species` LIKE ? AND `Domain_Group` LIKE ? LIMIT ?, 10";
$stmt = $dbh->prepare($query);
$param = array("%$q%", "%$q%", "%$q%", "%$sp%", "%$gr%", "$s");
$stmt->execute($param);
?>
<table class="table table-condensed">
<tbody>
<tr>
<td style="border: none;"><h5>Search Terms: <span class="text-uppercase"><?=$q?></span></h5></td>
<td style="border: none;"><h5>Species: <span class="text-uppercase"><?=$sp?></span></h5></td>
<td style="border: none;"><h5>PRM Family: <span class="text-uppercase">
<?php if(empty($gr)) { ?>
<?=$total_families.' found'?>
<?php } else { ?>
<?=$gr?>
<?php } ?>
</span></h5></td>
</tr>
<tr>
<td style="border: none;"><h5>Proteins Found: <?=$total_proteins?></h5></td>
<td style="border: none;"><h5>Domains Found: <?=$total?></h5></td>
<td style="border: none;"><h5>PWM Found: <?=$total_pwms?></h5></td>
</tr>
<tbody>
</table>
</div>
</div>
</div>
<div class="row">
<div class="col-md-10 col-md-offset-1">
<h4><strong>Search Results</strong></h4><hr>
<?php if ($total_pages > 1) { ?>
<div class="row">
<div class="col-md-4 col-md-offset-4">
<nav aria-label="...">
<ul class="pager">
<?php $link = "results.php?q={$q}&species={$sp}&group={$gr}&page="; ?>
<li><a href='<?=$link.'1'?>'>First</a></li>
<?php if(($page) > 1) { ?>
<li><a href='<?=$link.strval($page - 1)?>'>Previous</a></li>
<?php } ?>
<li>Page <?=$page?> of <?=$total_pages?></li>
<?php if(($page) < $total_pages) { ?>
<li><a href='<?=$link.strval($page + 1)?>'>Next</a></li>
<?php } ?>
<li><a href='<?=$link.$total_pages?>'>Last</a></li>
</ul>
</nav>
</div>
</div>
<?php } ?>
<div class="list-group">
<?php while ($row = $stmt->fetch()) { ?>
<h5 class="list-group-item-heading">
<strong>PRM Definition: </strong><?=$row['Protein_Name'].' '.$row['Domain_Begin'].'-'.$row['Domain_End']?> |
<!-- <strong>Protein Domain Name: </strong><?=$row['Protein_Name'].'_'.$row['Domain_Group'].$row['Domain_Number']?> | -->
<strong>Family: </strong><?=$row['Domain_Group']?> |
<strong>UNIPROT ID: </strong><a href="http://www.uniprot.org/uniprot/<?=$row['Uniprot_ID']?>" target="_blank"><?=$row['Uniprot_ID']?></a>
</h5>
<div class="list-group-item">
<div class="col-md-3">
<h5 style="font-weight:bold">Sequence logo</h5>
<?php if(file_exists('files/Logos/'.$row['Primary_ID'].'_1.png')) { ?>
<img src="files/Logos/<?=$row['Primary_ID']?>_1.png" class="img-thumbnail logo" data-element="<?=$row['Primary_ID']?>">
<?php
$i = 1;
while(true) {
$i = $i + 1;
if(!file_exists("files/Logos/".$row['Primary_ID']."_".$i.".png")) break;
}
?>
<span class="pager-bubble">
<?php for($j=1; $j<$i; $j++) { ?>
<i class="fa fa-lg fa-circle" data-count="<?=$j?>"></i>
<?php } ?>
</span>
<?php } else { ?>
<img src="files/Logos/<?=$row['Primary_ID']?>.png" class="img-thumbnail logo">
<?php } ?>
</div>
<div class="col-md-3">
<h5 style="font-weight:bold">Top Peptides Binders</h5>
<span class="links top-peptides">
<strong>Top ELISA-based peptide binders</strong>
<span class="seq">
<?php
if(trim($row['HAL']) != '' && $row['HAL'] != 'NA') echo str_replace(",",", ",$row['HAL']);
else echo '#N/A';
?>
</span>
<strong>Most abundant NGS peptides</strong>
<span class="seq">
<?php
if(trim($row['NGS']) != '' && $row['NGS'] != 'NA') echo str_replace(",",", ",$row['NGS']);
else echo '#N/A';
?>
</span>
</span>
</div>
<div class="col-md-3">
<h5 style="font-weight:bold">Closest Complex Structure</h5>
<a href="https://www.rcsb.org/pdb/explore/explore.do?structureId=<?=$row['PDB_ID']?>" target="_blank">
<img src="https://cdn.rcsb.org/images/rutgers/<?=substr($row['PDB_ID'],1,2)?>/<?=$row['PDB_ID']?>/<?=$row['PDB_ID']?>.pdb1-500.jpg" class="img-thumbnail structure">
</a>
</div>
<div class="col-md-3">
<h5 style="font-weight:bold">Downloads</h5>
<span class="links downloads">
<a href="network.php?gene=<?=$row['Protein_Name']?>">PWM pattern matches</a>
<?php if (file_exists('files/PWM/'.$row['Primary_ID'].'.dat')) { ?>
<a href="files/PWM/<?=$row['Primary_ID']?>.dat" target="_blank">Position Weight Matrix</a>
<?php } else if(file_exists('files/PWM/'.$row['Primary_ID'].'_1.dat')) { ?>
<span>
Position Weight Matrix
<?php
$i = 1;
while(true) {
echo "<a href='files/PWM/".$row['Primary_ID']."_".$i.".dat' target='_blank' style='padding: 0px 2px'>".$i."</a>";
$i = $i + 1;
if(!file_exists("files/PWM/".$row['Primary_ID']."_".$i.".dat")) break;
}
?>
</span>
<?php } ?>
<?php if(file_exists('files/ELISA/'.$row['Primary_ID'].'.fa')) { ?>
<a href="files/ELISA/<?=$row['Primary_ID']?>.fa" target="_blank">ELISA-based peptide binders</a>
<?php } else if (file_exists('files/ELISA/'.$row['Primary_ID'].'_1.fa')) { ?>
<span>
ELISA-based peptide binders
<?php
$i = 1;
while(true) {
echo "<a href='files/ELISA/".$row['Primary_ID']."_".$i.".fa' target='_blank' style='padding: 0px 2px'>".$i."</a>";
$i = $i + 1;
if(!file_exists("files/ELISA/".$row['Primary_ID']."_".$i.".fa")) break;
}
?>
</span>
<?php } ?>
<?php if(file_exists('files/NGS/'.$row['Primary_ID'].'.fa')) { ?>
<a href="files/NGS/<?=$row['Primary_ID']?>.fa" target="_blank">NGS peptides</a>
<?php } ?>
<?php if(file_exists('files/PDB/'.$row['Primary_ID'].'.txt')) { ?>
<a href="files/PDB/<?=$row['Primary_ID']?>.txt" target="_blank">Structural Similarities</a>
<?php } ?>
</span>
</div>
</div>
<?php } if ($total == 0) { ?>
<div class="list-group-item text-center">Nothing Found!</div>
<?php } ?>
</div>
</div>
</div>
<?php if ($total_pages > 1) { ?>
<div class="row">
<div class="col-md-4 col-md-offset-4">
<nav aria-label="...">
<ul class="pager">
<?php $link = "results.php?q={$q}&species={$sp}&group={$gr}&page="; ?>
<li><a href='<?=$link.'1'?>'>First</a></li>
<?php if(($page) > 1) { ?>
<li><a href='<?=$link.strval($page - 1)?>'>Previous</a></li>
<?php } ?>
<li>Page <?=$page?> of <?=$total_pages?></li>
<?php if(($page) < $total_pages) { ?>
<li><a href='<?=$link.strval($page + 1)?>'>Next</a></li>
<?php } ?>
<li><a href='<?=$link.$total_pages?>'>Last</a></li>
</ul>
</nav>
</div>
</div>
<?php } ?>
</div>
<script>
$(window).on('load', function () {
$('.logo').each(function () {
if (!this.complete || typeof this.naturalWidth === "undefined" || this.naturalWidth === 0) {
$(this).attr("src", "http://via.placeholder.com/800x300/fff/000?text=NO+LOGO+AVAILABLE");
$(this).next().hide();
}
});
$('.structure').each(function () {
if (!this.complete || typeof this.naturalWidth === "undefined" || this.naturalWidth === 0) {
$(this).attr("src", "http://via.placeholder.com/800x300/fff/000?text=NO+STRUCTURE+AVAILABLE");
$(this).parent().removeAttr("href");
}
});
$('.top-peptides').each(function () {
if($.trim($(this).html()) == "") {
$(this).hide();
}
});
});
$(document).ready(function() {
$('.fa-circle').on('click', function(){
$(this).parent().children().removeClass('fa-circle-thin').addClass('fa-circle');
$(this).removeClass('fa-circle').addClass('fa-circle-thin');
var count = $(this).data('count');
var el = $(this).parent().prev().data('element');
$(this).parent().prev().attr('src', 'files/Logos/' + el + '_' + count + '.png');
});
});
</script>
<?php include_once('partials/footer.php'); ?>
</body>
</html>