-
Notifications
You must be signed in to change notification settings - Fork 0
/
index_V1.php
377 lines (306 loc) · 15.1 KB
/
index_V1.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
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
<!DOCTYPE html>
<html>
<head>
<title>GeLoc</title>
<meta charset="utf-8">
<!--Bootstrap 4.4-->
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/css/bootstrap.min.css" integrity="sha384-Vkoo8x4CGsO3+Hhxv8T/Q5PaXtkKtu6ug5TOeNV6gBiFeWPGFN9MuhOf23Q9Ifjh" crossorigin="anonymous">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/popper.js@1.16.0/dist/umd/popper.min.js" integrity="sha384-Q6E9RHvbIyZFJoft+2mJbHaEWldlvI9IOYy5n3zV9zzTtmI3UksdQRVvoxMfooAo" crossorigin="anonymous"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/js/bootstrap.min.js" integrity="sha384-wfSDF2E50Y2D1uUdj0O3uMBJnjuUD4Ih7YwaYd1iqfktj0Uod8GCExl3Og8ifwB6" crossorigin="anonymous"></script>
<link href="https://stackpath.bootstrapcdn.com/bootswatch/4.4.1/sandstone/bootstrap.min.css" rel="stylesheet" integrity="sha384-ABdnjefqVzESm+f9z9hcqx2cvwvDNjfrwfW5Le9138qHCMGlNmWawyn/tt4jR4ba" crossorigin="anonymous">
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/d3/4.1.1/d3.min.js"></script>
<!-- <script src="https://cdn.jsdelivr.net/npm/ideogram@1.16.0/dist/js/ideogram.min.js"></script> -->
<!--Ideogram-->
<!-- <script src="https://cdn.jsdelivr.net/npm/ideogram@1.16.0/dist/js/ideogram.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/ideogram@1.19.0/dist/js/ideogram.min.js"></script> -->
<script src="https://cdn.jsdelivr.net/npm/ideogram@1.21.0/dist/js/ideogram.min.js"></script>
<!--D3JS-->
<script src="https://d3js.org/d3.v5.min.js"></script>
<!--GELOC-->
<!-- <script src="src/hidpi-canvas.min.js"></script> -->
<script src="src/main_V1.js" defer ></script>
<script type="text/javascript" src="src/html2canvas.js"></script>
<script type="text/javascript" src="src/canvas2image.js"></script>
<script src="https://d3js.org/d3-axis.v1.min.js"></script>
<!--SocketIO-->
<script src="node_modules/socket.io-client/dist/socket.io.js"></script>
<script>
var socket = io('http://195.221.173.169:4242');
var release = "current";
</script>
<link rel="stylesheet" type="text/css" href="src/css/gemo.css">
<link rel="shortcut icon" href="/gemo/public/img/favicon.ico">
</head>
<body>
<!--JUMBOTRON-->
<div class="jumbotron jumbo-bg">
<p class="lead">
<img src="./public/img/GeLoc_full.png"></img>
</p>
</div>
<!-- END OF JUMBOTRON-->
<div id="loader" class="triple-spinner" style="display:none;"></div>
<!--SIDEBAR-->
<div id="wrapper">
<div id="sidebar-wrapper">
<aside id="sidebar">
<ul id="sidemenu" class="sidebar-nav">
<!--HOME-->
<li id="homebutton">
<a class="accordion-toggle collapsed toggle-switch" data-toggle="collapse" href="#submenu-1">
<span class="sidebar-icon"><i class="fa fa-dashboard"></i></span>
<span class="sidebar-title">Home</span>
<b class="caret"></b>
</a>
<!-- <ul id="submenu-1" class="panel-collapse collapse panel-switch" role="menu">
</ul> -->
</li>
<!--DATA-->
<li>
<a class="accordion-toggle collapsed toggle-switch" data-toggle="collapse" href="#submenu-2">
<span class="sidebar-icon"><i class="fa fa-dashboard"></i></span>
<span class="sidebar-title">Browse data</span>
<b class="caret"></b>
</a>
<ul id="submenu-2" class="panel-collapse collapse show panel-switch" role="menu">
<li>
<!-- select accessions-->
<label for="selectAccession">Accession</label>
<select class="form-control-sm" id="selectAccession">
<option value=""></option>
<option value="Nipponbare">Nipponbare</option>
<option value="Kitaake">Kitaake</option>
</select>
<div id="switch" class="custom-control custom-switch">
<input type="checkbox" class="custom-control-input" id="readingSense" checked>
<label class="custom-control-label" for="readingSense">Show genes in reading sense</label>
</div>
<!-- search-->
<br/>
<div>
<input style="width:60%; display:inline-block;" id="keyword" class="form-control mr-sm-2" type="search" placeholder="Search by ID" aria-label="Search">
<button style="display:inline-block;" id="search" class="btn btn-outline-dark my-2 my-sm-0" type="submit">Search</button>
<div>
<div id="search_result_1" style="display: none; max-height: 200px; overflow: scroll;">
</div>
<div id="search_result_2" style="display: none; max-height: 200px; overflow: scroll;">
</div>
<!-- gene card -->
<div id="gene_card" style="display: none">
Gene card
</div>
<!-- legende flottante -->
<div id=floating_legend>
<button type="button" class="btn btn-dark btn-sm" style="display: none" id="legend_button" data-toggle="collapse" data-target="#legend_div" aria-expanded="false" aria-controls="legend_div">
Legend
</button>
<div class="collapse" id="legend_div" >
</div>
</div>
<!-- fin legende flottante -->
</li>
</ul>
</li>
<!-- Release -->
<li id="releasebutton">
<a class="accordion-toggle collapsed toggle-switch" data-toggle="collapse" href="#submenu-3">
<span class="sidebar-icon"><i class="fa fa-dashboard"></i></span>
<span class="sidebar-title">Releases</span>
<b class="caret"></b>
</a>
</li>
<!-- download -->
<li id="downloadbutton">
<a class="accordion-toggle collapsed toggle-switch" data-toggle="collapse" href="#submenu-4">
<span class="sidebar-icon"><i class="fa fa-dashboard"></i></span>
<span class="sidebar-title">Download</span>
<b class="caret"></b>
</a>
</li>
<!-- feedback -->
<li id="feedbackbutton">
<a class="accordion-toggle collapsed toggle-switch" data-toggle="collapse" href="#submenu-5">
<span class="sidebar-icon"><i class="fa fa-dashboard"></i></span>
<span class="sidebar-title">Send feedback</span>
<b class="caret"></b>
</a>
</li>
</ul>
</aside>
</div>
<!-- fin de la sidebar -->
<!-- Message navigateur -->
<div class="alert alert-secondary alert-dismissible fade show" role="alert">
Hello!
This Web site is optimized for viewing in Chrome.
To make the best use of GeLoc, we recommend you to download the latest Chrome version.
<button type="button" class="close" data-dismiss="alert" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<!-- Home -->
<div id="home" class="container">
<div id="welcome">
<!--JUMBOTRON-->
<div class="jumbotron jb_welcome">
<h1 class="display-2">Welcome to GeLoc</h1><br/>
</div><!--fin du jumbotron-->
<div id="home_text">
<p>
Plant resistance genes are mainly encoded by three large Leucine-Rich Repeat (LRR)-containing receptor (LRR-CR) families: the LRR-Receptor-Like Kinase (LRR-RLK), LRR-Receptor-Like Protein (LRR-RLP) and Nucleotide-binding LRR Receptor (NLR).
</p>
<p>
We have proposed manually curated annotations of these genes for reference rice genomes: nipponbare <a href="https://rapdb.dna.affrc.go.jp/download/irgsp1.html">(IRGSP-01) </a> and kitaake <a href="https://phytozome-next.jgi.doe.gov/info/OsativaKitaake_v3_1"> (KitaakeX-v3.1)</a> japonica cultivars.
</p>
<p>
These annotations include genes tagged as non-canonical because they contain nonsense mutations, as opposed to canonical genes that contain all expected features to be functional (see Gottin et al. 2021 for further details).
</p>
<p>
Geloc provides convenient tools to visualised and download these annotation data.
</p>
</div>
<div class="row justify-content-md-center">
<div class="col-sm-3">
<div class="card border-dark">
<img class="card-img-top" src="./public/img/select.gif" alt="Card image cap">
<div class="card-footer bg-transparent border-dark">Select an accession to display</div>
</div>
</div>
<div class="col-sm-1"></div>
<div class="col-sm-3">
<div class="card border-dark">
<img class="card-img-top" src="./public/img/click_chr.gif" alt="Card image cap">
<div class="card-footer bg-transparent border-dark">Click on a chromosome to browse through</div>
</div>
</div>
<div class="col-sm-1"></div>
<div class="col-sm-3">
<div class="card border-dark">
<img class="card-img-top" src="./public/img/move_range.gif" alt="Card image cap">
<div class="card-footer bg-transparent border-dark">Navigate and view genes</div>
</div>
</div>
</div>
<div id="home_text">
<p>Please cite:</p>
<div id="gene_card">
<p>
Gottin, C., Dievart, A., Summo, M., Droc, G., Périn, C., Ranwez, V. and Chantret, N. (2021), A New Comprehensive Annotation of Leucine-Rich Repeat-Containing Receptors in Rice. The Plant Journal. Accepted Author Manuscript. https://doi.org/10.1111/tpj.15456
</p>
</div>
</div>
</div> <!-- fin welcome -->
<!-- releases -->
<div id="releases" class="home_content" style="display: none">
<h3>Releases</h3><br/>
<p><strong>2021-05-03 - Latest</strong></p>
<p><strong>2021-01-22</strong> <a href="previous.php">Browse this release here</a></p>
</div>
<!-- download -->
<div id="download_section" class="home_content" style="display: none">
<h3>Download</h3><br/>
<p><strong>Files "Peptides" and "CDS":</strong></p>
<p>These files contain amino acid and nuclotide sequences for LRR-CR genes.
For genes experiencing frameshift, the one or two bases that cause the frameshift are avoided in order
to have nucleotide sequence that can be translated.
</p>
<p><strong>Files "cDNA":</strong></p>
<p>These files contain nucleotide sequences for the complete LRR-CR genes without intron.
In the case of genes experiencing frameshift, the sequences cannot be translated in comprehensive protein
sequences. For all other genes, the files "CDS" and "cDNA" retrieve the same nucleotide seqences.
</p>
<p><strong>Files "cDNA_wFrameshift": </strong></p>
<p>These files contain nucleotide sequences of non-canonical genes. In the case
of genes experiencing frameshift, the sequence is completed with one or two "!" characters at the position
of the frameshift in order to conserve the right reading frame (also used by V. Ranwez et al. for the
MACSE programs). The translation of these sequences will create amino acid sequences with frameshift
caracterised by an "X" character.
</p>
<p><strong>Nipponbare</strong></p>
<a href="./data_current/dl/Nipponbare_IDs.txt.zip" download="Nipponbare_IDs.txt.zip">Nipponbare_IDs.txt.zip</a><br/>
<a href="./data_current/dl/Oryza_Kitaake_LRR-CR_cDNA__20210503.fasta.zip" download="Oryza_Kitaake_LRR-CR_cDNA__20210503.fasta.zip">Oryza_Kitaake_LRR-CR_cDNA__20210503.fasta.zip</a><br/>
<a href="./data_current/dl/Oryza_Nipponbare_IRGSP-1.0_LRR-CR_cDNA__20210503.fasta.zip" download="Oryza_Nipponbare_IRGSP-1.0_LRR-CR_cDNA__20210503.fasta.zip">Oryza_Nipponbare_IRGSP-1.0_LRR-CR_cDNA__20210503.fasta.zip</a><br/>
<a href="./data_current/dl/Oryza_Nipponbare_IRGSP-1.0_LRR-CR_CDS__20210503.fasta.zip" download="Oryza_Nipponbare_IRGSP-1.0_LRR-CR_CDS__20210503.fasta.zip">Oryza_Nipponbare_IRGSP-1.0_LRR-CR_CDS__20210503.fasta.zip</a><br/>
<a href="./data_current/dl/Oryza_Nipponbare_IRGSP-1.0_LRR-CR_PEP__20210503.fasta.zip" download="Oryza_Nipponbare_IRGSP-1.0_LRR-CR_PEP__20210503.fasta.zip">Oryza_Nipponbare_IRGSP-1.0_LRR-CR_PEP__20210503.fasta.zip</a><br/>
<a href="./data_current/dl/Oryza_Nipponbare_IRGSP-1.0_LRR-CR_cDNA_wFrameshift___20210503.fasta.zip" download="Oryza_Nipponbare_IRGSP-1.0_LRR-CR_cDNA_wFrameshift___20210503.fasta.zip">Oryza_Nipponbare_IRGSP-1.0_LRR-CR_cDNA_wFrameshift___20210503.fasta.zip</a><br/>
<br/>
<p><strong>Kitaake</strong></p>
<a href="./data_current/dl/Kitaake_IDs.txt.zip" download="Kitaake_IDs.txt.zip">Kitaake_IDs.txt.zip</a><br/>
<a href="./data_current/dl/ORYSJ_kitaake_LRR-CR__20210503.gff.zip" download="ORYSJ_kitaake_LRR-CR__20210503.gff.zip">ORYSJ_kitaake_LRR-CR__20210503.gff.zip</a><br/>
<a href="./data_current/dl/Oryza_Kitaake_LRR-CR_cDNA__20210503.fasta.zip" download="Oryza_Kitaake_LRR-CR_cDNA__20210503.fasta.zip">Oryza_Kitaake_LRR-CR_cDNA__20210503.fasta.zip</a><br/>
<a href="./data_current/dl/Oryza_Kitaake_LRR-CR_CDS__20210503.fasta.zip" download="Oryza_Kitaake_LRR-CR_CDS__20210503.fasta.zip">Oryza_Kitaake_LRR-CR_CDS__20210503.fasta.zip</a><br/>
<a href="./data_current/dl/Oryza_Kitaake_LRR-CR_cDNA_wFrameshift__20210503.fasta.zip" download="Oryza_Kitaake_LRR-CR_cDNA_wFrameshift__20210503.fasta.zip">Oryza_Kitaake_LRR-CR_cDNA_wFrameshift__20210503.fasta.zip</a><br/>
<br/>
<p><strong>Orthologous</strong></p>
<a href="./data_current/dl/Nip_Kit_ortho.txt.zip" download="Nip_Kit_ortho.txt.zip">Nip_Kit_ortho.txt.zip</a><br/>
</div>
<!-- feedback -->
<div id="feedback" style="display: none">
<h3>Feedback</h3><br/>
<form>
<div class="form-group">
<label for="exampleFormControlInput1">Email address</label>
<input type="email" class="form-control" id="email" placeholder="name@example.com">
</div>
<div class="form-group">
<label for="exampleFormControlSelect1">How was your experience on our website ?</label>
<select class="form-control" id="xp">
<option>Great</option>
<option>Good</option>
<option>Ok</option>
<option>Bad</option>
</select>
</div>
<div class="form-group">
<label for="exampleFormControlTextarea1">Tell us what you think</label>
<textarea class="form-control" id="feedbackmessage" rows="3"></textarea>
</div>
<button id="submitfeedback" type="submit" class="btn btn-outline-dark">Submit</button>
<button id="submitfeedbackok" style="display: none" class="btn btn-outline-success" disabled>Thank you :)</button>
</form>
</div>
</div>
<!-- Div DataViz globale -->
<div id="DataViz" style="display: none">
<!-- button show / hide global view -->
<div style="display: none" id="show-hide">
<button type="button" class="btn btn-outline-dark" data-toggle="collapse" data-target="#page-content-wrapper" aria-expanded="false" aria-controls="collapseExample"> Show / hide all chromosomes</button>
</div>
<div id="page-content-wrapper" class="ideo_container_global collapse show">
<!-- The ideogram goes here. -->
</div>
<div class="ideo_container_chr" max-width="1000px">
<!-- The ideogram chromosome goes here. -->
</div>
<!-- Selected region -->
<div id="selected_region" style="display: none;">
Selected region:
<br/>
<span id="from"></span> - <span id="to"></span>
(extent: <span id="extent"></span> base pairs)
</div>
<div class="zoom_global" style="display: none; width:100%; overflow: scroll;">
<!-- The zoomed view goes here. -->
<canvas id="zoom_global" height="300" width="1000">
Désolé, votre navigateur ne prend pas en charge <canvas>.
</canvas>
<canvas id="zoom_selected" height="80" width="1000">
</canvas>
</div>
<div id="cds_div" class="cds" style="display: none; width:100%; max-height:500px;max-width:1200px;overflow: scroll;">
<!-- The CDS view goes here. -->
<canvas id="cds" height="1200" width="1200">
Désolé, votre navigateur ne prend pas en charge <canvas>.
</canvas>
</div>
<div id="chr_region" heigth="300px" style="display: none;">
<!-- The GFF info goes here. -->
<div class='container'>
<pre id="gffResult" style="width:100%; max-height: 300px;max-width:1200px;overflow: scroll;">
</pre>
</div>
</div>
</div>
</body>
</html>