forked from vidjil/vidjil
-
Notifications
You must be signed in to change notification settings - Fork 0
/
index.html
306 lines (250 loc) · 16.7 KB
/
index.html
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
<!doctype html>
<!--
This file is part of "Vidjil" <http://bioinfo.lille.inria.fr/vidjil>, V(D)J repertoire browsing and analysis
Copyright (C) 2013, 2014 by Marc Duez <marc.duez@lifl.fr> and the Vidjil Team
Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
"Vidjil" is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
"Vidjil" is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with "Vidjil". If not, see <http://www.gnu.org/licenses/>
-->
<html>
<head>
<meta charset="utf-8">
<title>Vidjil</title>
<link rel="shortcut icon" href="./images/favicon-v.ico" type="image/x-icon">
<link rel="icon" href="./images/favicon-v.ico" type="image/x-icon">
<link rel="stylesheet" type="text/css" href="css/fonts/ubuntu/stylesheet.css" />
<link rel="stylesheet" type="text/css" href="css/fonts/ubuntu-mono/stylesheet.css" />
<link rel="stylesheet" type="text/css" href="css/icons/fontello/css/fontello.css" />
<link rel="stylesheet" type="text/css" href="css/icons/fontello/css/animation.css" />
<link id="palette" rel="stylesheet" type="text/css" href="css/light.css" />
<link id="seg_highlight" rel="stylesheet" type="text/css" href="css/segmenter_highlight.css" />
<script data-main="js/app.js" src="js/lib/require.js"></script>
</head>
<body>
<div id="file_menu" >
<span class="closeButton" onclick="cancel();">X</span>
<h2>Vidjil <span class='logo'>(beta)</span> – V(D)J repertoire browsing and analysis</h2>
Data file (.vidjil):<br/>
<input id="upload_json" type="file" name="json" /></br>
<p class='help'>The .vidjil file stores a set of clones on several points.</p>
Analysis file (.analysis, optional):<br/>
<input id="upload_pref" type="file" name="pref" /></br>
<p class='help'>The .analysis file stores all parameters set by the user (tags, colors, manual clusters).</p>
<button onclick="document.getElementById('file_menu').style.display='none';
m.load('upload_json','upload_pref', 200)">start</button>
</div>
<div id="axis_choice" >
<span class="closeButton" onclick="cancel();">X</span>
<h2>analysis menu</h2>
Analysis file:<br/>
<input id="upload_analysis" type="file" name="analysis" /></br></br>
<button onclick="document.getElementById('axis_choice').style.display='none';
m.loadAnalysis('upload_analysis');">start</button>
</div>
<div id="upload_summary" style="" class="menu" onmouseover="showSelector('upload_summary_selector');" onmouseout="hideSelector();">
<span id="upload_summary_label">upload</span>
<div id="upload_summary_selector" class="selector"><div>
</div></div>
</div>
<!-- TOP-CONTAINER -->
<div id="top-container" onmouseout="hideSelector()">
<div id="menu-container">
<div class="menu" id="top_info">
<!--Div is filled programmatically -->
</div>
<div class="menu" id="db_menu" onmouseover="showSelector('dbSelector');" style="display : none">patients
<div id="dbSelector" class="selector"><div>
<div class="menu_box">
<a class="buttonSelector" onclick="javascript:db.call('patient/index')">open patient list</a>
</div>
<div class="menu_box">
<div id="last_loaded_file">
</div>
</div>
</div></div>
</div>
<div class="menu" id="static_file_menu" onmouseover="showSelector('fileSelector');" style="display : none">file
<div id="fileSelector" class="selector"><div>
<div class="menu_box">
<div id="upload_list">
</div>
</div>
</div></div>
</div>
<div class="menu" id="demo_file_menu" onmouseover="showSelector('demoSelector');">import/export
<div id="demoSelector" class="selector"><div>
<div class="menu_box">
<a id="import_data_anchor" id="import_data" class="buttonSelector" onclick="javascript:loadData()">import data (.vidjil)</a>
<a id="import_data_analysis" id="import_analysis" class="buttonSelector" onclick="javascript:loadAnalysis()">import analysis</a>
</div>
<!--<a class="buttonSelector" onclick="javascript:m.resetAnalysis()">reset analysis</a> -->
<!--<a class="buttonSelector" onclick="javascript:reset()">reset all</a> -->
<div class="menu_box">
<a class="buttonSelector" id="export_sample_report" onclick="javascript:report.reportHTMLdiag()">export report (sample)</a>
<a class="buttonSelector" id="export_monitor_report" onclick="javascript:report.reportHTML()">export report (monitor)</a>
</div>
<div class="menu_box">
<a class="buttonSelector" id="export_analysis" onclick="javascript:m.saveAnalysis()">export analysis</a>
<a class="buttonSelector" id="export_svg1" onclick="javascript:graph.resize(1400,800);m.exportSVG('visu2_svg')">export SVG graph</a>
<a class="buttonSelector" id="export_svg2" onclick="javascript:sp.resize(1400,800);sp.fastForward();m.exportSVG('visu_svg')">export SVG plot</a>
<a class="buttonSelector" id="export_csv" onclick="javascript:m.exportCSV()">export csv (visible clones)</a>
<a class="buttonSelector" id="export_fasta" onclick="javascript:m.exportFasta()">export fasta (selected clones)</a>
</div>
</div></div>
</div>
<div class="menu" id="cluster_menu" onmouseover="showSelector('clusterSelector');" > cluster
<div id="clusterSelector" class="selector"><div>
<a class="buttonSelector" onclick="m.restoreClusters();">clones merged by user</a>
<a class="buttonSelector" onclick="m.resetClusters();">reset all user clones</a>
<a class="buttonSelector" onclick="m.clusterBy(function(id){return m.clone(id).getGene(5)});">cluster by V/5' </a>
<a class="buttonSelector" onclick="m.clusterBy(function(id){return m.clone(id).getGene(3)});">cluster by J/3' </a>
<a class="buttonSelector" onclick="m.clusterBy(function(id){return m.clone(id).germline});">cluster by locus </a>
<a class="buttonSelector devel-mode" onclick="m.similarity_builder.DBscan(95,0.001);">cluster by DBscan (experimental) </a>
<a class="buttonSelector" onclick="m.similarity_builder.cluster_me(95,0.1);">cluster by similarity </a>
<div id="clusterby_button"> </div>
</div></div>
</div>
<div class="menu" id="color_menu" onmouseover="showSelector('colorSelector');" > color by
<div class="div-menu-selector"><select class="menu-selector" onchange="m.changeColorMethod(this.value)">
<option value="Tag">tag</option>
<option value="V">V/5'</option>
<option value="J">J/3'</option>
<option value="N">N</option>
<option value="system" id="color_system_button">locus/germline</option>
<option value="abundance">abundance</option>
<option value="productive">productivity</option>
</select></div>
</div>
<div class="menu" id="filter_menu" onmouseenter="builder.build_displaySelector();" onmouseover="showSelector('filterSelector');" > filter
<div id="filterSelector" class="selector"><div>
<div class="menu_box">
<span id="top_label"></span></br>
<input id="top_slider" type="range" min="5" max="100" step="5" value="10" onchange="m.displayTop(this.value)" />
</div>
<div class="menu_box">
tag visibility</br>
<ul id="tagList">
</ul>
</div>
</div></div>
</div>
<div class="menu" id="settings_menu" onmouseenter="builder.build_settings();" onmouseover=" showSelector('settingsSelector');" > settings
<div id="settingsSelector" class="selector"><div>
<div class="menu_box">
normalization</br>
<form name="normalize_list" id="normalize_list">
</form>
</div>
<div class="menu_box">
normalization method</br>
<div class="buttonSelector" onclick="m.changeNormMethod('constant')" ><input type="radio" name="normalize_method" value="constant" checked >constant</input></div>
<div class="buttonSelector" onclick="m.changeNormMethod('to-100')" ><input type="radio" name="normalize_method" value="to-100">to 100%</input></div>
</div>
<div class="menu_box">
size display</br>
<div class="buttonSelector" onclick="m.changeNotation('scientific', true)"><input type="radio" name="notation" value="scientific" >scientific notation</input></div>
<div class="buttonSelector" onclick="m.changeNotation('percent', true)"><input type="radio" name="notation" value="percent" checked>percent</input></div>
</div>
<div class="menu_box">
point key</br>
<div class="buttonSelector" onclick="m.changeTimeFormat('name', true)"><input type="radio" name="time" value="name" checked>name</input></div>
<div class="buttonSelector" onclick="m.changeTimeFormat('short_name', true)"><input type="radio" name="time" value="short_name" checked>name (short)</input></div>
<div class="buttonSelector" onclick="m.changeTimeFormat('sampling_date', true)"><input type="radio" name="time" value="sampling_date" >sampling date</input></div>
<div class="buttonSelector" onclick="m.changeTimeFormat('delta_date', true)"><input type="radio" name="time" value="delta_date">day after first sample</input></div>
</div>
<!--
<div class="submenu" id="system_menu" style="display:none">
<div class="menu_box">
selected locus/germline (for the grid)</br>
<ul id="germline_list">
</ul>
</div>
</div>
-->
<!--menu graph/dbscan -->
<div class="submenu" style="display:none">
<div class="menu_box">
<div id="DBSCANEpsSlider">
<input id="changeEps" type="range" min="0" max="40" step="1" value="0" onchange="m.changeEps(this.value)" />
</div>
</div>
<div class="menu_box">
<div id="DBSCANNbrSlider">
<input id="changeNbr" type="range" min="0" max="100" step="1" value="0" onchange="m.changeNbr(this.value)" />
</div>
</div>
<div class="menu_box">
<div id="EditDistanceSlider">
</br>
<input id="displayMax_slider" type="range" min="1" max="20" step="1" value="10" onchange="sp.displayDistanceMax(this.value)" style="display:none"/>
</div>
</div>
</div>
</div></div>
</div>
<div id="debug_menu" class="menu" onmouseover="showSelector('adminSelector');" style="display : none"> development
<div id="adminSelector" class="selector"><div>
<input type="checkbox" onclick=" this.checked ? $('#fps').css('display', '') : $('#fps').css('display', 'none');">display fps</input></br>
<input type="checkbox" onclick=" this.checked ? console.openLog() : console.closeLog() ;">log</input>
<div class="buttonSelector" onclick="m.changeTimeFormat('delta_date_no_zero', true)"><input type="radio" name="time" value="delta_date_no_zero">day after first sample (no zero)</input></div>
</div></div>
</div>
</div>
<div id="logo" style="float: right;" onclick="console.log({'type': 'popup', 'default':'welcome'})">Vidjil <span class='logo'>(beta)</span></div>
<div class="menu" style="float: right" onmouseover="showSelector('helpSelector');"> help
<div id="helpSelector" class="selector"><div>
<a class="buttonSelector getHelp" onclick="report.sendMail()">get support</a>
<a class="buttonSelector" href="http://www.vidjil.org/doc/browser.html" target="_blank">manual</a>
<a class="buttonSelector" href="http://www.vidjil.org/doc/tutorial/mastering-vidjil.html" target="_blank">tutorial</a>
</div></div>
</div>
<div style="float: right" class="menu" onmouseover="showSelector('paletteSelector');"> palette
<div id="paletteSelector" class="selector"><div>
<a class="buttonSelector" onclick="changeStyle('solarizeL')">light</a>
<a class="buttonSelector" onclick="changeStyle('display')">light (presentation)</a>
<a class="buttonSelector" onclick="changeStyle('solarizeD')">dark</a>
</div></div>
</div>
<div style="float: right; margin: 5px;" id='live-ajax'></div>
<div id="fps" style="float: right; display: none"> </div>
<div id="header_messages" class="message_container header"></div>
<!--
<div class="menu" style="float: right; margin-right:100px"><span style="padding: 4px 5px; background-color: #fef6e3; font-family: ubuntulight;">
<b>Maintenance:</b> Vidjil will be offline Tuesday 7, 11:00 → 13:00 CEST. Thank you for your understanding.
</span></div>
-->
</div>
<!-- fin top-container-->
<!-- MID-CONTAINER -->
<div id="mid-container" onmouseover="hideSelector()">
<!-- LEFT-CONTAINER -->
<div id="left-container">
<div id="info-row"><div id="info"> </div></div>
<div id="list-row"><div id="list"> </div></div>
<div id="data-row"><div id="data"> </div></div>
</div>
<!-- fin left-container -->
<div id="vertical-separator"></div>
<!-- RIGHT-CONTAINER -->
<div id="right-container"></div>
<!-- VISU-CONTAINER -->
<div id="visu-container">
<div id="visu2"></div>
<div id="visu-separator" >...</div>
<div id="visu" onclick=""></div>
</div>
</div>
<!-- fin mid-container -->
<!-- BOT-CONTAINER / SEGMENTER-CONTAINER -->
<div id="bot-container"> </div>
<form id="form"></form>
</body>
</html>