File: spectrum.html

package info (click to toggle)
toppic 1.3.0%2Bdfsg1-4
  • links: PTS, VCS
  • area: main
  • in suites: bookworm, bullseye, sid
  • size: 44,588 kB
  • sloc: cpp: 61,030; javascript: 33,937; xml: 8,121; ansic: 2,437; python: 755; sh: 76; makefile: 20
file content (301 lines) | stat: -rw-r--r-- 12,989 bytes parent folder | download
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
<html>
<head>
<META http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title>spectrum</title>
<link rel="stylesheet" href="file:///usr/share/fonts-font-awesome/css/font-awesome.min.css">
<link rel="stylesheet" type="text/css" href="../css/lib/jquery.dataTables.css"/>
<link rel="stylesheet" type="text/css" href="../css/lib/bootstrap.min.css">
<link rel="stylesheet" type="text/css" href="../css/lib/nav_bar.css">
<link rel="stylesheet" type="text/css" href="css/spectrum.css">
<link rel="stylesheet" type="text/css" href="css/modal.css">
<link rel="stylesheet" type="text/css" href="css/svg.css">

<script type="text/javascript" src="../js/lib/popper.min.js"></script>
<script type="text/javascript" src="../js/lib/jQuery_3_4.js"></script>
<script type="text/javascript" src="../js/lib/jquery.dataTables.js"></script>
<script src="../js/lib/d3/d3.js"></script>
<script src="../js/lib/bootstrap/bootstrap.min.js" ></script>
<script src="js/UI_helpers/helper.js" ></script>
<script src="js/UI_helpers/seqofexecution.js" ></script>
<script src="js/UI_helpers/onclickandeventhandler.js" ></script>
<script src="js/UI_helpers/getmasstableofselectedions.js" ></script>
<script src="js/UI_helpers/constants.js" ></script>

<script src="../js/spectrum_graph/invokespectrum.js" ></script>
<script src="../js/spectrum_graph/spectrumgraph.js" ></script>
<script src="../js/spectrum_graph/spectrumparameters.js" ></script>
<script src="../js/spectrum_graph/spectrumdownload.js" ></script>

<script src="js/distribution_calc/emassanddistribution.js" ></script>
<script src="js/distribution_calc/isotopes.js" ></script>
<script src="js/distribution_calc/aminoaciddistribution.js" ></script>
<script src="js/distribution_calc/molecularformulae.js" ></script>

<script src="js/sequence_svg/coordinates_util.js" ></script>
<script src="js/sequence_svg/drawsvg.js" ></script>

<script src="js/matched_peaks/matchedpeaks.js" ></script>
<script src="js/matched_peaks/calculateprefixandsuffixmass.js" ></script>

<script src="js/mass_shift/utilfunctions.js" ></script>
<script src="js/mass_shift/massshift.js" ></script>
<script src="js/mass_shift/commonFixedPtms.js" ></script>
<!--V2 changes-->

<script src="js/ion_fragmentation/iontabledata.js" ></script>

<!--Save Image-->
<script src="js/download/FileSaver.js" ></script>
<script src="js/download/saveImage.js" ></script>

<!--Set Data to HTML-->
<script src="js/UI_helpers/setvaluestohtml.js" ></script>

<!--draw nav bar-->
<script src="../visual/js/util/navBar.js" ></script>



<script>
 $(document).ready(function(){
	var peakAndIntensityList = JSON.parse(window.localStorage.getItem('peakAndIntensityList'));
	var massAndIntensityList = JSON.parse(window.localStorage.getItem('massAndIntensityList'));
	var sequence = JSON.parse(window.localStorage.getItem('sequence'));
	var l_fixedPtmList = JSON.parse(window.localStorage.getItem('fixedPtmList'));

	if(peakAndIntensityList != null && massAndIntensityList != null
		&& sequence != null)
	{	
		let SetValuesToHtmlObj = new SetValuesToHtml(peakAndIntensityList,massAndIntensityList,sequence,l_fixedPtmList);
		SetValuesToHtmlObj.setDataToPeakAndIntensity();
		SetValuesToHtmlObj.setDataToMassAndIntensity();
		SetValuesToHtmlObj.setDataToSequence();
		SetValuesToHtmlObj.setFixedMasses();
	}
	onLoadOfHTML();
	localStorage.clear();
});
</script>
<style>
</style>
</head>
<body>
	<div id="nav-bar"></div>
<br></br><br></br><br>
<div class="container">
	<div class="flex-rectangle">
		<div class="row">
			<div class="col-md-4 col-lg-4">
				<h5>Peaks <img src="images/info.png" id="peakintensityinfo" alt="nfo"></h5>
				<textarea id="peakdata" class="form-control col-xs-12" rows="10" cols="50"></textarea>
			</div>
			<div class="col-md-3 col-lg-3">
				<h5>Masses & intensities <img src="images/info.png" id="massintensityinfo" alt="info"></h5>
				<textarea id="data" class="form-control col-xs-12" rows="10" cols="50"></textarea>
			</div>
			<div class="col-md-3 col-lg-3">
				<h5>Ion types <img src="images/info.png" id="ionfragmentinfo" alt="info"></h5>
				<table class="table table-sm table-bordered ionfragments">
				<tbody>
					<tr>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="nterminus" value="-27.9949" id="a">
							<label class="custom-control-label" for="a">a</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="nterminus" value="-46.0149" id="a1">
							<label class="custom-control-label" for="a1" >a-H<sub>2</sub>O</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="nterminus" value="-45.02542" id="a2">
							<label class="custom-control-label" for="a2" >a-NH<sub>3</sub></label>
							</div></td>	
					</tr>
					<tr>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="nterminus" value="0" id="b" checked>
							<label class="custom-control-label" for="b" >b</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="nterminus" value="-18.02" id="b1">
							<label class="custom-control-label" for="b1" >b-H<sub>2</sub>O</label>
							</div></td>
						<td><div class="custom-control custom-checkbox" >
							<input type="checkbox" class="custom-control-input" name="nterminus" value="-17.03052" id="b2">
							<label class="custom-control-label" for="b2" >b-NH<sub>3</sub></label>
							</div></td>
					</tr>
					<tr>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="nterminus"  value="17.0266" id="c">
							<label class="custom-control-label" for="c">c</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="nterminus"  value="-0.9934" id="c1">
							<label class="custom-control-label" for="c1" >c-H<sub>2</sub>O</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input"  name="nterminus"value="-0.00392" id="c2">
							<label class="custom-control-label" for="c2" >c-NH<sub>3</sub></label>
							</div></td>
					</tr>
					<tr>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="cterminus" value="43.99" id="x">
							<label class="custom-control-label" for="x" >x</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="cterminus" value="25.97" id="x1">
							<label class="custom-control-label" for="x1" >x-H<sub>2</sub>O</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="cterminus" value="26.95948" id="x2">
							<label class="custom-control-label" for="x2" >x-NH<sub>3</sub></label>
							</div></td>
					</tr>
					<tr>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="cterminus" value="18.0106" id="y" checked>
							<label class="custom-control-label" for="y" >y</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="cterminus" value="0" id="y1">
							<label class="custom-control-label" for="y1" >y-H<sub>2</sub>O</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="cterminus" value="0.98008" id="y2">
							<label class="custom-control-label" for="y2" >y-NH<sub>3</sub></label>
							</div></td>
					</tr>
					<tr>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="cterminus" value="0.984" id="z">
							<label class="custom-control-label" for="z" >z</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="cterminus" value="-17.026" id="z1">
							<label class="custom-control-label" for="z1" >z-H<sub>2</sub>O</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
							<input type="checkbox" class="custom-control-input" name="cterminus" value="-16.04652" id="z2">
							<label class="custom-control-label" for="z2" >z-NH<sub>3</sub></label>
							</div></td>
					</tr>
					<tr>
						<td><div class="custom-control custom-checkbox">
								<input type="checkbox" class="custom-control-input" name="cterminus" value="1.9919" id="z_">
								<label class="custom-control-label" for="z_">z&deg;</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
								<input type="checkbox" class="custom-control-input" name="cterminus" value="-16.018664" id="z_1">
								<label class="custom-control-label" for="z_1" >z&deg;-H<sub>2</sub>O</label>
							</div></td>
						<td><div class="custom-control custom-checkbox">
								<input type="checkbox" class="custom-control-input" name="cterminus" value="-15.03862" id="z_2">
								<label class="custom-control-label" for="z_2" >z&deg;-NH<sub>3</sub></label>
							</div></td>	
						</tr>
				</tbody>
				</table>
			</div>
			<div class="col-md-2 col-lg-2">
					<h5>Fixed PTMs <img src="images/info.png" id="fixedptminfo" alt="info"></h5>
				<div class="fixedptmslist">
				<select class="browser-default custom-select" id="dropdownMenuLink">
				</select>	
				<button type="button" class="btn btn-default btn-sm addnewrow">
						<i class="fa fa-plus" ></i>
				</button>
					<form class="form-inline mr-auto">
						<div id = "fixedptmslist" > 
							<br>
						</div>
					</form>
				</div>
			</div>
		</div>
		<div class="row">
			<h5>&nbsp;&nbsp;&nbsp;Protein sequence <img src="images/info.png" id="sequenceinfo" alt="info"></h5>
		</div>
		<div class="row">
			<div class="col-8">
					<textarea id="sequencedata" class="form-control col-xs-8"></textarea>
			</div>
			<div class="col-4">
				<form class="form-inline float-sm-right error_input">
					<select class = "form-control error_dropdown" id="error_dropdown">
					<option value="masserror">Mass error</option>
					<option value="ppmerror">PPM error</option>
					</select>&nbsp;&nbsp;
					<input class="form-control" type="text" id="errorval" /> &nbsp;&nbsp;
					<h6><text  class="form-group" id="errorunit">Da&nbsp;&nbsp;</text></h6>
					<button id="submit" type="button" class="btn btn-primary form-group">submit</button>
				</form>
			</div>
		</div>
	</div> 
	<br>
		<div class="row">
			<div class="col-6">
				<h6 id="totalseqmass_h6" style="display:none"><text>Molecular Mass:&nbsp;</text><text id="totalmass">0</text></h6>
			</div>
			<div class="col-6">
					<div class="dropdown dropleft float-right">
					<button type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown" id="svg_download" style="display:none">
					  Download
					</button>
					<div class="dropdown-menu">
					  <a class="dropdown-item" href="#!" id="seq_download_png">Download as PNG</a>
					  <a class="dropdown-item" href="#!" id="seq_download_svg">Download as SVG</a>
					</div>
				  </div>
			</div>
		</div>
		<div class="row">
			<div class="rounded mx-auto d-block" >
				<svg id = "seqsvg" style="background-color:white;display:none"></svg>
			</div>	
		</div>
	<div class="row">
		
	</div>
	<div class="row">
		<svg id = "spectrum" height="250" width = "1000" style="background-color:white;display:none"></svg>
	</div>
	<div class="row" id="peakCount" style="display:none">
		<div class="col-2 pull-left" >
			<a id="all_peak_count" href="#!" onclick="showAllPeaks();">All Peaks</a>
		</div>
		<div class="col-2 pull-left" >
			<a id="matched_peak_count" href="#!" onclick="showMatchedPeaks();">Matched Peaks</a>
		</div>
		<div class="col-3 pull-left" >
			<a id="unmatched_peak_count" href="#!" onclick="showNonMatchedPeaks();">Non Matched Peaks</a>
		</div>
		<div class="col-5 pull-right" >
			<button type="button" class="btn btn-primary float-right" id="hide_table">Hide Table</button>
		</div>
	</div>
	<div class="row">
		<div class="col-12" >
			<div id="divtableContainer" >
			</div>
		</div>
	</div>
	<br>
	<div class="row">
			<h4 id="h_fragmentedtable" style="display:none">Theoritical Fragment Masses</h4>
		<div class="col-12" >
			<div id="divselectediontablecontainer" >
			</div>
		</div>
	</div>
</div>
<br>
<footer class="page-footer font-small blue">
	<div class="footer-copyright text-center py-3">© 2019 Copyright: The Trustees of 
		<a href="https://www.iu.edu/" target="#">Indiana University</a>
	</div>
</footer>
</body>
</html>