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
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
|
<HTML>
<HEAD>
<TITLE>TransitionTSVReader Class Reference</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<A href="index.html">Home</A> ·
<A href="classes.html">Classes</A> ·
<A href="annotated.html">Annotated Classes</A> ·
<A href="modules.html">Modules</A> ·
<A href="functions_func.html">Members</A> ·
<A href="namespaces.html">Namespaces</A> ·
<A href="pages.html">Related Pages</A>
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<!-- Generated by Doxygen 1.8.5 -->
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html">TransitionTSVReader</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#nested-classes">Classes</a> |
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pri-types">Private Types</a> |
<a href="#pri-methods">Private Member Functions</a> |
<a href="#pri-static-attribs">Static Private Attributes</a> |
<a href="classOpenMS_1_1TransitionTSVReader-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">TransitionTSVReader Class Reference</div> </div>
</div><!--header-->
<div class="contents">
<p>This class can convert TraML and TSV files into each other.
<a href="classOpenMS_1_1TransitionTSVReader.html#details">More...</a></p>
<p><code>#include <<a class="el" href="TransitionTSVReader_8h_source.html">OpenMS/ANALYSIS/OPENSWATH/TransitionTSVReader.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for TransitionTSVReader:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1TransitionTSVReader.png" usemap="#TransitionTSVReader_map" alt=""/>
<map id="TransitionTSVReader_map" name="TransitionTSVReader_map">
<area href="classOpenMS_1_1ProgressLogger.html" title="Base class for all classes that want to report their progess. " alt="ProgressLogger" shape="rect" coords="0,0,132,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a61fec279b0e1353549a798fd81584851"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#a61fec279b0e1353549a798fd81584851">convertTargetedExperimentToTSV</a> (const char *filename, <a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> &targeted_exp)</td></tr>
<tr class="memdesc:a61fec279b0e1353549a798fd81584851"><td class="mdescLeft"> </td><td class="mdescRight">Write out a targeted experiment (TraML structure) into a tsv file. <a href="#a61fec279b0e1353549a798fd81584851">More...</a><br/></td></tr>
<tr class="separator:a61fec279b0e1353549a798fd81584851"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a586860c61e9394bbd63a95d067ae60bf"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#a586860c61e9394bbd63a95d067ae60bf">convertTSVToTargetedExperiment</a> (const char *filename, <a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> &targeted_exp)</td></tr>
<tr class="memdesc:a586860c61e9394bbd63a95d067ae60bf"><td class="mdescLeft"> </td><td class="mdescRight">Read in a tsv file and construct a targeted experiment (TraML structure) <a href="#a586860c61e9394bbd63a95d067ae60bf">More...</a><br/></td></tr>
<tr class="separator:a586860c61e9394bbd63a95d067ae60bf"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8fd604357b531cdb9a207ed8914ff7ac"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#a8fd604357b531cdb9a207ed8914ff7ac">validateTargetedExperiment</a> (<a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> &targeted_exp)</td></tr>
<tr class="memdesc:a8fd604357b531cdb9a207ed8914ff7ac"><td class="mdescLeft"> </td><td class="mdescRight">Validate a <a class="el" href="classOpenMS_1_1TargetedExperiment.html" title="This class stores an prediction of an SRM/MRM transition. ">TargetedExperiment</a> (check that all ids are unique) <a href="#a8fd604357b531cdb9a207ed8914ff7ac">More...</a><br/></td></tr>
<tr class="separator:a8fd604357b531cdb9a207ed8914ff7ac"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a2a106011aec95b2013d7a545f2063d01">ProgressLogger</a> ()</td></tr>
<tr class="memdesc:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a2a106011aec95b2013d7a545f2063d01">More...</a><br/></td></tr>
<tr class="separator:a2a106011aec95b2013d7a545f2063d01 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a19c882d907f90f7f88c7436d82cd2a13">~ProgressLogger</a> ()</td></tr>
<tr class="memdesc:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a19c882d907f90f7f88c7436d82cd2a13">More...</a><br/></td></tr>
<tr class="separator:a19c882d907f90f7f88c7436d82cd2a13 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#acc3538c5284777d8702ccaefeb61e74c">setLogType</a> (<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> type) const </td></tr>
<tr class="memdesc:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Sets the progress log that should be used. The default type is NONE! <a href="#acc3538c5284777d8702ccaefeb61e74c">More...</a><br/></td></tr>
<tr class="separator:acc3538c5284777d8702ccaefeb61e74c inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a67024cdd5c34ec571baecabd8f783310">getLogType</a> () const </td></tr>
<tr class="memdesc:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Returns the type of progress log being used. <a href="#a67024cdd5c34ec571baecabd8f783310">More...</a><br/></td></tr>
<tr class="separator:a67024cdd5c34ec571baecabd8f783310 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af1c45ecd71b5041b70319249e8e73591">startProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> begin, <a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> end, const <a class="el" href="classOpenMS_1_1String.html">String</a> &label) const </td></tr>
<tr class="memdesc:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Initializes the progress display. <a href="#af1c45ecd71b5041b70319249e8e73591">More...</a><br/></td></tr>
<tr class="separator:af1c45ecd71b5041b70319249e8e73591 inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a8852277abd03220cc7b80d6c1bed6fed">setProgress</a> (<a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> value) const </td></tr>
<tr class="memdesc:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Sets the current progress. <a href="#a8852277abd03220cc7b80d6c1bed6fed">More...</a><br/></td></tr>
<tr class="separator:a8852277abd03220cc7b80d6c1bed6fed inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a1cc1012b0cdaea97f58d571af1ff45de">endProgress</a> () const </td></tr>
<tr class="memdesc:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="mdescLeft"> </td><td class="mdescRight">Ends the progress display. <a href="#a1cc1012b0cdaea97f58d571af1ff45de">More...</a><br/></td></tr>
<tr class="separator:a1cc1012b0cdaea97f58d571af1ff45de inherit pub_methods_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-types"></a>
Private Types</h2></td></tr>
<tr class="memitem:abb7606c8e2c53bab61362619f44b3c11"><td class="memItemLeft" align="right" valign="top">typedef std::vector<br class="typebreak"/>
< <a class="el" href="classOpenMS_1_1TargetedExperiment.html#a6be5011e53737493e15d175f5d4a1d03">OpenMS::TargetedExperiment::Protein</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#abb7606c8e2c53bab61362619f44b3c11">ProteinVectorType</a></td></tr>
<tr class="separator:abb7606c8e2c53bab61362619f44b3c11"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a87ab7393ee32c7d08b5db91c4d1a95d8"><td class="memItemLeft" align="right" valign="top">typedef std::vector<br class="typebreak"/>
< <a class="el" href="classOpenMS_1_1TargetedExperiment.html#aa81ff3b563bdf4fff6c1e4e265f2275e">OpenMS::TargetedExperiment::Peptide</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#a87ab7393ee32c7d08b5db91c4d1a95d8">PeptideVectorType</a></td></tr>
<tr class="separator:a87ab7393ee32c7d08b5db91c4d1a95d8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7a9324ee2f11d04b8cab4e4d9c6d750e"><td class="memItemLeft" align="right" valign="top">typedef std::vector<br class="typebreak"/>
< <a class="el" href="classOpenMS_1_1ReactionMonitoringTransition.html">OpenMS::ReactionMonitoringTransition</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#a7a9324ee2f11d04b8cab4e4d9c6d750e">TransitionVectorType</a></td></tr>
<tr class="separator:a7a9324ee2f11d04b8cab4e4d9c6d750e"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:aa833c768dfa512c4f73624c0e4393a02"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#aa833c768dfa512c4f73624c0e4393a02">readTSVInput_</a> (const char *filename, std::vector< <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> > &transition_list)</td></tr>
<tr class="memdesc:aa833c768dfa512c4f73624c0e4393a02"><td class="mdescLeft"> </td><td class="mdescRight">read TSV input with columns in defined order <a href="#aa833c768dfa512c4f73624c0e4393a02">More...</a><br/></td></tr>
<tr class="separator:aa833c768dfa512c4f73624c0e4393a02"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae1dca04a3eba945e66a9a57c71459444"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#ae1dca04a3eba945e66a9a57c71459444">getTSVHeader</a> (std::string &line, char &delimiter, std::vector< std::string > header, std::map< std::string, int > &header_dict)</td></tr>
<tr class="memdesc:ae1dca04a3eba945e66a9a57c71459444"><td class="mdescLeft"> </td><td class="mdescRight">determine separater in a CSV file and check for correct headers <a href="#ae1dca04a3eba945e66a9a57c71459444">More...</a><br/></td></tr>
<tr class="separator:ae1dca04a3eba945e66a9a57c71459444"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2454582cdfc6bc2a3dd0c069c0e54320"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#a2454582cdfc6bc2a3dd0c069c0e54320">readUnstructuredTSVInput_</a> (const char *filename, std::vector< <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> > &transition_list)</td></tr>
<tr class="memdesc:a2454582cdfc6bc2a3dd0c069c0e54320"><td class="mdescLeft"> </td><td class="mdescRight">read tab or comma separated input with columns defined by their column headers only <a href="#a2454582cdfc6bc2a3dd0c069c0e54320">More...</a><br/></td></tr>
<tr class="separator:a2454582cdfc6bc2a3dd0c069c0e54320"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a26336fdbb6f46a7dc7aff771036e95b3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#a26336fdbb6f46a7dc7aff771036e95b3">cleanUpTransition</a> (<a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> &mytransition)</td></tr>
<tr class="memdesc:a26336fdbb6f46a7dc7aff771036e95b3"><td class="mdescLeft"> </td><td class="mdescRight">do post-processing on read input data (removing quotes etc) <a href="#a26336fdbb6f46a7dc7aff771036e95b3">More...</a><br/></td></tr>
<tr class="separator:a26336fdbb6f46a7dc7aff771036e95b3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8ce28c35947a6b833052e7ca10e374e4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#a8ce28c35947a6b833052e7ca10e374e4">TSVToTargetedExperiment_</a> (std::vector< <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> > &transition_list, <a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> &exp)</td></tr>
<tr class="memdesc:a8ce28c35947a6b833052e7ca10e374e4"><td class="mdescLeft"> </td><td class="mdescRight">store a list of <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> objects properly in a <a class="el" href="classOpenMS_1_1TargetedExperiment.html" title="This class stores an prediction of an SRM/MRM transition. ">TargetedExperiment</a> <a href="#a8ce28c35947a6b833052e7ca10e374e4">More...</a><br/></td></tr>
<tr class="separator:a8ce28c35947a6b833052e7ca10e374e4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afbe7a1ec351b818b34c226762711912e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#afbe7a1ec351b818b34c226762711912e">createTransition_</a> (std::vector< <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> >::iterator &tr_it, <a class="el" href="classOpenMS_1_1ReactionMonitoringTransition.html">OpenMS::ReactionMonitoringTransition</a> &rm_trans)</td></tr>
<tr class="separator:afbe7a1ec351b818b34c226762711912e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aff69ae29d16408dd461156aae5209302"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#aff69ae29d16408dd461156aae5209302">createProtein_</a> (std::vector< <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> >::iterator &tr_it, <a class="el" href="classOpenMS_1_1TargetedExperiment.html#a6be5011e53737493e15d175f5d4a1d03">OpenMS::TargetedExperiment::Protein</a> &protein)</td></tr>
<tr class="separator:aff69ae29d16408dd461156aae5209302"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa2a3155d2826f904abb7d1c07649d3f6"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#aa2a3155d2826f904abb7d1c07649d3f6">createPeptide_</a> (std::vector< <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> >::iterator &tr_it, <a class="el" href="classOpenMS_1_1TargetedExperiment.html#aa81ff3b563bdf4fff6c1e4e265f2275e">OpenMS::TargetedExperiment::Peptide</a> &peptide)</td></tr>
<tr class="separator:aa2a3155d2826f904abb7d1c07649d3f6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac2986b272b16fac328a333b39f80231c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#ac2986b272b16fac328a333b39f80231c">add_modification_</a> (std::vector< <a class="el" href="structOpenMS_1_1TargetedExperimentHelper_1_1Peptide_1_1Modification.html">TargetedExperiment::Peptide::Modification</a> > &mods, int location, <a class="el" href="classOpenMS_1_1ResidueModification.html">ResidueModification</a> &rmod, const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="separator:ac2986b272b16fac328a333b39f80231c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a85a9ff8578e6fd351357da24caebdf49"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#a85a9ff8578e6fd351357da24caebdf49">writeTSVOutput_</a> (const char *filename, <a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> &targeted_exp)</td></tr>
<tr class="memdesc:a85a9ff8578e6fd351357da24caebdf49"><td class="mdescLeft"> </td><td class="mdescRight">write a <a class="el" href="classOpenMS_1_1TargetedExperiment.html" title="This class stores an prediction of an SRM/MRM transition. ">TargetedExperiment</a> to a file <a href="#a85a9ff8578e6fd351357da24caebdf49">More...</a><br/></td></tr>
<tr class="separator:a85a9ff8578e6fd351357da24caebdf49"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-static-attribs"></a>
Static Private Attributes</h2></td></tr>
<tr class="memitem:a690d775311dd827693a4ec63940061e8"><td class="memItemLeft" align="right" valign="top">static const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#a690d775311dd827693a4ec63940061e8">strarray</a> []</td></tr>
<tr class="separator:a690d775311dd827693a4ec63940061e8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af5dd4beb8177d4b7414973699c2973bc"><td class="memItemLeft" align="right" valign="top">static const std::vector<br class="typebreak"/>
< std::string > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TransitionTSVReader.html#af5dd4beb8177d4b7414973699c2973bc">header_names</a></td></tr>
<tr class="separator:af5dd4beb8177d4b7414973699c2973bc"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
Additional Inherited Members</h2></td></tr>
<tr class="inherit_header pub_types_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pub_types_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Public Types inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> { <a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca3ab34dd50405af2d5a62627d572f7860">CMD</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87ca73c6901c7c648a6a735770bc038bb26a">GUI</a>,
<a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87cac157bdf0b85a40d2619cbc8bc1ae5fe2">NONE</a>
}</td></tr>
<tr class="memdesc:af67907baa897e9fb84df0cb89795b87c"><td class="mdescLeft"> </td><td class="mdescRight">Possible log types. <a href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">More...</a><br/></td></tr>
<tr class="separator:af67907baa897e9fb84df0cb89795b87c inherit pub_types_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_attribs_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a7c691d7de2a43bc5606e96cb15da3641 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1ProgressLogger.html#af67907baa897e9fb84df0cb89795b87c">LogType</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a7c691d7de2a43bc5606e96cb15da3641">type_</a></td></tr>
<tr class="separator:a7c691d7de2a43bc5606e96cb15da3641 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a56589612e0e4164bf80c3918a087d05a">begin_</a></td></tr>
<tr class="separator:a56589612e0e4164bf80c3918a087d05a inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0c749bf4e621699b7a5c45ae22c2fa90 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a0c749bf4e621699b7a5c45ae22c2fa90">end_</a></td></tr>
<tr class="separator:a0c749bf4e621699b7a5c45ae22c2fa90 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aec57b26e143202dc119a41592e075932 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gae113cb41304c6692c7bf5d0624dc6f0f">SignedSize</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#aec57b26e143202dc119a41592e075932">value_</a></td></tr>
<tr class="separator:aec57b26e143202dc119a41592e075932 inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a76072b3919abcf01141ba68da8a001fd inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">QProgressDialog * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a76072b3919abcf01141ba68da8a001fd">dlg_</a></td></tr>
<tr class="separator:a76072b3919abcf01141ba68da8a001fd inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6d9750520313ea7f843d7a49cb2e9e5f inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1StopWatch.html">StopWatch</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a6d9750520313ea7f843d7a49cb2e9e5f">stop_watch_</a></td></tr>
<tr class="separator:a6d9750520313ea7f843d7a49cb2e9e5f inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a79bacf60c4109d7517590441c7f85f9c inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">time_t </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a79bacf60c4109d7517590441c7f85f9c">last_invoke_</a></td></tr>
<tr class="separator:a79bacf60c4109d7517590441c7f85f9c inherit pro_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_static_attribs_classOpenMS_1_1ProgressLogger"><td colspan="2" onclick="javascript:toggleInherit('pro_static_attribs_classOpenMS_1_1ProgressLogger')"><img src="closed.png" alt="-"/> Static Protected Attributes inherited from <a class="el" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a></td></tr>
<tr class="memitem:a94eb3ef5ef94b83eb348dd00a2b53119 inherit pro_static_attribs_classOpenMS_1_1ProgressLogger"><td class="memItemLeft" align="right" valign="top">static int </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1ProgressLogger.html#a94eb3ef5ef94b83eb348dd00a2b53119">recursion_depth_</a></td></tr>
<tr class="separator:a94eb3ef5ef94b83eb348dd00a2b53119 inherit pro_static_attribs_classOpenMS_1_1ProgressLogger"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>This class can convert TraML and TSV files into each other. </p>
<p>The TSV are tab-separated and need to have the following columns:</p>
<p>PrecursorMz (float) ProductMz (float) Tr_calibrated (float) transition_name (free text, needs to be unique for each transition [in this file]) CE (float) LibraryIntensity (float) transition_group_id (free text, designates the transition group [e.g. peptide] to which this transition belongs) decoy (1==decoy, 0== no decoy; determines whether the transition is a decoy transition or not) PeptideSequence (free text, sequence only (no modifications) ) ProteinName (free text) Annotation (free text, e.g. y7) FullUniModPeptideName (free text, should contain modifications*) MissedCleavages Replicates NrModifications PrecursorCharge (integer) Labelgroup (free text, e.g. heavy or light) </p>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
<a class="anchor" id="a87ab7393ee32c7d08b5db91c4d1a95d8"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">typedef std::vector<<a class="el" href="classOpenMS_1_1TargetedExperiment.html#aa81ff3b563bdf4fff6c1e4e265f2275e">OpenMS::TargetedExperiment::Peptide</a>> <a class="el" href="classOpenMS_1_1TransitionTSVReader.html#a87ab7393ee32c7d08b5db91c4d1a95d8">PeptideVectorType</a></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<a class="anchor" id="abb7606c8e2c53bab61362619f44b3c11"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">typedef std::vector<<a class="el" href="classOpenMS_1_1TargetedExperiment.html#a6be5011e53737493e15d175f5d4a1d03">OpenMS::TargetedExperiment::Protein</a>> <a class="el" href="classOpenMS_1_1TransitionTSVReader.html#abb7606c8e2c53bab61362619f44b3c11">ProteinVectorType</a></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<a class="anchor" id="a7a9324ee2f11d04b8cab4e4d9c6d750e"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">typedef std::vector<<a class="el" href="classOpenMS_1_1ReactionMonitoringTransition.html">OpenMS::ReactionMonitoringTransition</a>> <a class="el" href="classOpenMS_1_1TransitionTSVReader.html#a7a9324ee2f11d04b8cab4e4d9c6d750e">TransitionVectorType</a></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a class="anchor" id="ac2986b272b16fac328a333b39f80231c"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void add_modification_ </td>
<td>(</td>
<td class="paramtype">std::vector< <a class="el" href="structOpenMS_1_1TargetedExperimentHelper_1_1Peptide_1_1Modification.html">TargetedExperiment::Peptide::Modification</a> > & </td>
<td class="paramname"><em>mods</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>location</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1ResidueModification.html">ResidueModification</a> & </td>
<td class="paramname"><em>rmod</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td>
<td class="paramname"><em>name</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<a class="anchor" id="a26336fdbb6f46a7dc7aff771036e95b3"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void cleanUpTransition </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> & </td>
<td class="paramname"><em>mytransition</em></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>do post-processing on read input data (removing quotes etc) </p>
</div>
</div>
<a class="anchor" id="a61fec279b0e1353549a798fd81584851"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void convertTargetedExperimentToTSV </td>
<td>(</td>
<td class="paramtype">const char * </td>
<td class="paramname"><em>filename</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> & </td>
<td class="paramname"><em>targeted_exp</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Write out a targeted experiment (TraML structure) into a tsv file. </p>
</div>
</div>
<a class="anchor" id="a586860c61e9394bbd63a95d067ae60bf"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void convertTSVToTargetedExperiment </td>
<td>(</td>
<td class="paramtype">const char * </td>
<td class="paramname"><em>filename</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> & </td>
<td class="paramname"><em>targeted_exp</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Read in a tsv file and construct a targeted experiment (TraML structure) </p>
</div>
</div>
<a class="anchor" id="aa2a3155d2826f904abb7d1c07649d3f6"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void createPeptide_ </td>
<td>(</td>
<td class="paramtype">std::vector< <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> >::iterator & </td>
<td class="paramname"><em>tr_it</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1TargetedExperiment.html#aa81ff3b563bdf4fff6c1e4e265f2275e">OpenMS::TargetedExperiment::Peptide</a> & </td>
<td class="paramname"><em>peptide</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<a class="anchor" id="aff69ae29d16408dd461156aae5209302"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void createProtein_ </td>
<td>(</td>
<td class="paramtype">std::vector< <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> >::iterator & </td>
<td class="paramname"><em>tr_it</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1TargetedExperiment.html#a6be5011e53737493e15d175f5d4a1d03">OpenMS::TargetedExperiment::Protein</a> & </td>
<td class="paramname"><em>protein</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<a class="anchor" id="afbe7a1ec351b818b34c226762711912e"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void createTransition_ </td>
<td>(</td>
<td class="paramtype">std::vector< <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> >::iterator & </td>
<td class="paramname"><em>tr_it</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1ReactionMonitoringTransition.html">OpenMS::ReactionMonitoringTransition</a> & </td>
<td class="paramname"><em>rm_trans</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<a class="anchor" id="ae1dca04a3eba945e66a9a57c71459444"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void getTSVHeader </td>
<td>(</td>
<td class="paramtype">std::string & </td>
<td class="paramname"><em>line</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">char & </td>
<td class="paramname"><em>delimiter</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">std::vector< std::string > </td>
<td class="paramname"><em>header</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">std::map< std::string, int > & </td>
<td class="paramname"><em>header_dict</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>determine separater in a CSV file and check for correct headers </p>
</div>
</div>
<a class="anchor" id="aa833c768dfa512c4f73624c0e4393a02"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void readTSVInput_ </td>
<td>(</td>
<td class="paramtype">const char * </td>
<td class="paramname"><em>filename</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">std::vector< <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> > & </td>
<td class="paramname"><em>transition_list</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>read TSV input with columns in defined order </p>
</div>
</div>
<a class="anchor" id="a2454582cdfc6bc2a3dd0c069c0e54320"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void readUnstructuredTSVInput_ </td>
<td>(</td>
<td class="paramtype">const char * </td>
<td class="paramname"><em>filename</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">std::vector< <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> > & </td>
<td class="paramname"><em>transition_list</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>read tab or comma separated input with columns defined by their column headers only </p>
</div>
</div>
<a class="anchor" id="a8ce28c35947a6b833052e7ca10e374e4"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void TSVToTargetedExperiment_ </td>
<td>(</td>
<td class="paramtype">std::vector< <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> > & </td>
<td class="paramname"><em>transition_list</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> & </td>
<td class="paramname"><em>exp</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>store a list of <a class="el" href="structOpenMS_1_1TransitionTSVReader_1_1TSVTransition.html">TSVTransition</a> objects properly in a <a class="el" href="classOpenMS_1_1TargetedExperiment.html" title="This class stores an prediction of an SRM/MRM transition. ">TargetedExperiment</a> </p>
</div>
</div>
<a class="anchor" id="a8fd604357b531cdb9a207ed8914ff7ac"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void validateTargetedExperiment </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> & </td>
<td class="paramname"><em>targeted_exp</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Validate a <a class="el" href="classOpenMS_1_1TargetedExperiment.html" title="This class stores an prediction of an SRM/MRM transition. ">TargetedExperiment</a> (check that all ids are unique) </p>
</div>
</div>
<a class="anchor" id="a85a9ff8578e6fd351357da24caebdf49"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void writeTSVOutput_ </td>
<td>(</td>
<td class="paramtype">const char * </td>
<td class="paramname"><em>filename</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1TargetedExperiment.html">OpenMS::TargetedExperiment</a> & </td>
<td class="paramname"><em>targeted_exp</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>write a <a class="el" href="classOpenMS_1_1TargetedExperiment.html" title="This class stores an prediction of an SRM/MRM transition. ">TargetedExperiment</a> to a file </p>
</div>
</div>
<h2 class="groupheader">Member Data Documentation</h2>
<a class="anchor" id="af5dd4beb8177d4b7414973699c2973bc"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">const std::vector<std::string> header_names</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">static</span><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<a class="anchor" id="a690d775311dd827693a4ec63940061e8"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">const char* strarray[]</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">static</span><span class="mlabel">private</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
</div><!-- contents -->
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<TABLE width="100%" border="0">
<TR>
<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>
|
