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
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
|
<HTML>
<HEAD>
<TITLE>MzXMLHandler.h Source File</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="dir_e770f0cf77e550adde3f44739ef529fe.html">include</a></li><li class="navelem"><a class="el" href="dir_6a63c4937d4da007e55fff5dcf71e0f8.html">OpenMS</a></li><li class="navelem"><a class="el" href="dir_d1695c75ee0aa48d87e52f45c7decd7a.html">FORMAT</a></li><li class="navelem"><a class="el" href="dir_e3cfd30209955a8faf482f155ddb826e.html">HANDLERS</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="headertitle">
<div class="title">MzXMLHandler.h</div> </div>
</div><!--header-->
<div class="contents">
<a href="MzXMLHandler_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: Andreas Bertsch $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: Marc Sturm $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_FORMAT_HANDLERS_MZXMLHANDLER_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FORMAT_HANDLERS_MZXMLHANDLER_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <<a class="code" href="ProgressLogger_8h.html">OpenMS/CONCEPT/ProgressLogger.h</a>></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <<a class="code" href="Base64_8h.html">OpenMS/FORMAT/Base64.h</a>></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor">#include <<a class="code" href="PeakFileOptions_8h.html">OpenMS/FORMAT/OPTIONS/PeakFileOptions.h</a>></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#include <<a class="code" href="XMLHandler_8h.html">OpenMS/FORMAT/HANDLERS/XMLHandler.h</a>></span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor">#include <<a class="code" href="String_8h.html">OpenMS/DATASTRUCTURES/String.h</a>></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <stack></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> </div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> {</div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keyword">class </span>MetaInfoInterface;</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span> </div>
<div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keyword">namespace </span>Internal</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  {</div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00060"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html"> 60</a></span>  <span class="keyword">class </span><a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler</a> :</div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a></div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  {</div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a265fc94e4af4dab38234d47a0132342b">MzXMLHandler</a>(MapType& exp, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& version, <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a>& logger) :</div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span>  <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a2f223274d440404ba700768cd15ef661">XMLHandler</a>(filename, version),</div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a21e306967405afb217201901a2d75351">exp_</a>(&exp),</div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">cexp_</a>(0),</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">decoder_</a>(),</div>
<div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a189e2aea7a4b8bbfcefbf62176d0966c">peak_count_</a>(0),</div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae22f2dafc17fa5b139b6805a58a01b67">char_rest_</a>(),</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a81dc4d91ca22493e81272673e507a8c4">skip_spectrum_</a>(<span class="keyword">false</span>),</div>
<div class="line"><a name="l00075"></a><span class="lineno"> 75</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a1d9a2d74c791b49639ee41852966f0a3">spec_write_counter_</a>(1),</div>
<div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">logger_</a>(logger)</div>
<div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  {</div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a009a30591b3297275a4db1359fcd82ed">init_</a>();</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span>  }</div>
<div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div>
<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a49a0a656327c327bd73a9eac5d4b2698"> 82</a></span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a49a0a656327c327bd73a9eac5d4b2698">MzXMLHandler</a>(<span class="keyword">const</span> MapType& exp, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& filename, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1String.html">String</a>& version, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a>& logger) :</div>
<div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html">XMLHandler</a>(filename, version),</div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a21e306967405afb217201901a2d75351">exp_</a>(0),</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">cexp_</a>(&exp),</div>
<div class="line"><a name="l00086"></a><span class="lineno"> 86</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">decoder_</a>(),</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a189e2aea7a4b8bbfcefbf62176d0966c">peak_count_</a>(0),</div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae22f2dafc17fa5b139b6805a58a01b67">char_rest_</a>(),</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a81dc4d91ca22493e81272673e507a8c4">skip_spectrum_</a>(false),</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a1d9a2d74c791b49639ee41852966f0a3">spec_write_counter_</a>(1),</div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">logger_</a>(logger)</div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  {</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a009a30591b3297275a4db1359fcd82ed">init_</a>();</div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  }</div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div>
<div class="line"><a name="l00097"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ab0e6ea8a2659622ef3bcd7da7ce4a22c"> 97</a></span>  <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ab0e6ea8a2659622ef3bcd7da7ce4a22c">~MzXMLHandler</a>()</div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  {</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  }</div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> </div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> </div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a8df65a3d6767516b62d0e4c84a14a4f4">endElement</a>(<span class="keyword">const</span> XMLCh* <span class="keyword">const</span> uri, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> local_name, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> qname);</div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> </div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aa1612242e2b5ea583324fadd8f0e5198">startElement</a>(<span class="keyword">const</span> XMLCh* <span class="keyword">const</span> uri, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> local_name, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> qname, <span class="keyword">const</span> xercesc::Attributes& attributes);</div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span>  <span class="comment">// Docu in base class</span></div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a742bdba7e6348fe6c549aada2a116944">characters</a>(<span class="keyword">const</span> XMLCh* <span class="keyword">const</span> chars, <span class="keyword">const</span> XMLSize_t length);</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> </div>
<div class="line"><a name="l00113"></a><span class="lineno"> 113</span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a0038ff865ac073e00ca829d977f2ccdf">writeTo</a>(std::ostream& os);</div>
<div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div>
<div class="line"><a name="l00116"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a2d6d13f6b8cb30e7943d4996e9ef2af7"> 116</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a2d6d13f6b8cb30e7943d4996e9ef2af7">setOptions</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a>& options)</div>
<div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  {</div>
<div class="line"><a name="l00118"></a><span class="lineno"> 118</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a654a0b5941d937e303c64bc9e732baec">options_</a> = options;</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  }</div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span> </div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="comment">// initialize members (call from C'tor)</span></div>
<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a009a30591b3297275a4db1359fcd82ed"> 123</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a009a30591b3297275a4db1359fcd82ed">init_</a>()</div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  {</div>
<div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>.resize(6);</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="comment">//Polarity</span></div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"any;+;-"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[0]);</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  <span class="comment">//Scan type</span></div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  <span class="comment">// is no longer used cv_terms_[1] is empty now</span></div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="comment">//Ionization method</span></div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";ESI;EI;CI;FAB;;;;;;;;;;;;;APCI;;;;;;;;MALDI"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[2]);</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[2].resize(<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4afca6a564be564def43e05f3204a973e3">IonSource::SIZE_OF_IONIZATIONMETHOD</a>);</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  <span class="comment">//Mass analyzer</span></div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";Quadrupole;Quadrupole Ion Trap;;;TOF;Magnetic Sector;FT-ICR;"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[3]);</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[3].resize(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a7925ff36af091300c66ad1f9615dbdc6">MassAnalyzer::SIZE_OF_ANALYZERTYPE</a>);</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  <span class="comment">//Detector</span></div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";EMT;;;Faraday Cup;;;;;Channeltron;Daly;Microchannel plate"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[4]);</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[4].resize(<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a441c9a986459d5abed57acdcb0899409">IonDetector::SIZE_OF_TYPE</a>);</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="comment">//Resolution method</span></div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">";FWHM;TenPercentValley;Baseline"</span>).<a class="code" href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">split</a>(<span class="charliteral">';'</span>, <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[5]);</div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">cv_terms_</a>[5].resize(<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a11053909f1f8edf7b9ccc41c1417ecf6a143a6a9882aaf613c6f529b976da6eea">MassAnalyzer::SIZE_OF_RESOLUTIONMETHOD</a>);</div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  <span class="comment">/* // OLD:</span></div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span> <span class="comment"> cv_terms_.resize(6);</span></div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> <span class="comment"> //Polarity</span></div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span> <span class="comment"> String("any;+;-").split(';',cv_terms_[0]);</span></div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> <span class="comment"> //Scan type</span></div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> <span class="comment"> // is no longer used cv_terms_[1] is empty now</span></div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> <span class="comment"> //Ionization method</span></div>
<div class="line"><a name="l00149"></a><span class="lineno"> 149</span> <span class="comment"> String(";ESI;EI;CI;FAB;TSP;MALDI;FD;FI;PD;SI;TI;API;ISI;CID;CAD;HN;APCI;APPI;ICP").split(';',cv_terms_[2]);</span></div>
<div class="line"><a name="l00150"></a><span class="lineno"> 150</span> <span class="comment"> //Mass analyzer</span></div>
<div class="line"><a name="l00151"></a><span class="lineno"> 151</span> <span class="comment"> String(";Quadrupole;Quadrupole Ion Trap;;;TOF;Magnetic Sector;FT-ICR;").split(';',cv_terms_[3]);</span></div>
<div class="line"><a name="l00152"></a><span class="lineno"> 152</span> <span class="comment"> //Detector</span></div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span> <span class="comment"> String(";EMT;Daly;;Faraday Cup;;;;Channeltron").split(';',cv_terms_[4]);</span></div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span> <span class="comment"> //Resolution method</span></div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span> <span class="comment"> String(";FWHM;TenPercentValley;Baseline").split(';',cv_terms_[5]);</span></div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span> <span class="comment"> */</span></div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  }</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span> </div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> </div>
<div class="line"><a name="l00162"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884"> 162</a></span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">MapType::PeakType</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884">PeakType</a>;</div>
<div class="line"><a name="l00164"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a066042ae14211da37d4fa66d466bfa3e"> 164</a></span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a066042ae14211da37d4fa66d466bfa3e">SpectrumType</a>;</div>
<div class="line"><a name="l00165"></a><span class="lineno"> 165</span> </div>
<div class="line"><a name="l00166"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a2b299003c15ddc54383dec1745f54944"> 166</a></span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html#a6d64276a665c3c0dca8fb4ade3c8b477">SpectrumType::Iterator</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a2b299003c15ddc54383dec1745f54944">PeakIterator</a>;</div>
<div class="line"><a name="l00167"></a><span class="lineno"> 167</span> </div>
<div class="line"><a name="l00169"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a21e306967405afb217201901a2d75351"> 169</a></span>  MapType* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a21e306967405afb217201901a2d75351">exp_</a>;</div>
<div class="line"><a name="l00171"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae19606cee74ec0ac3662fcfba274cbd0"> 171</a></span>  <span class="keyword">const</span> MapType* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">cexp_</a>;</div>
<div class="line"><a name="l00172"></a><span class="lineno"> 172</span> </div>
<div class="line"><a name="l00174"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a654a0b5941d937e303c64bc9e732baec"> 174</a></span>  <a class="code" href="classOpenMS_1_1PeakFileOptions.html">PeakFileOptions</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a654a0b5941d937e303c64bc9e732baec">options_</a>;</div>
<div class="line"><a name="l00175"></a><span class="lineno"> 175</span> </div>
<div class="line"><a name="l00178"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3"> 178</a></span>  <a class="code" href="classOpenMS_1_1Base64.html">Base64</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">decoder_</a>;</div>
<div class="line"><a name="l00179"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a189e2aea7a4b8bbfcefbf62176d0966c"> 179</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a189e2aea7a4b8bbfcefbf62176d0966c">peak_count_</a>;</div>
<div class="line"><a name="l00180"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a11010cea213654791e0211426489563b"> 180</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a11010cea213654791e0211426489563b">precision_</a>;</div>
<div class="line"><a name="l00181"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aec2ce57bef42db3fc6b2df2b3d3c9e6a"> 181</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aec2ce57bef42db3fc6b2df2b3d3c9e6a">compressionType_</a>;</div>
<div class="line"><a name="l00182"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae22f2dafc17fa5b139b6805a58a01b67"> 182</a></span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae22f2dafc17fa5b139b6805a58a01b67">char_rest_</a>;</div>
<div class="line"><a name="l00184"></a><span class="lineno"> 184</span> </div>
<div class="line"><a name="l00186"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a81dc4d91ca22493e81272673e507a8c4"> 186</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a81dc4d91ca22493e81272673e507a8c4">skip_spectrum_</a>;</div>
<div class="line"><a name="l00187"></a><span class="lineno"> 187</span> </div>
<div class="line"><a name="l00189"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a1d9a2d74c791b49639ee41852966f0a3"> 189</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a1d9a2d74c791b49639ee41852966f0a3">spec_write_counter_</a>;</div>
<div class="line"><a name="l00190"></a><span class="lineno"> 190</span> </div>
<div class="line"><a name="l00192"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e"> 192</a></span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ProgressLogger.html">ProgressLogger</a>& <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">logger_</a>;</div>
<div class="line"><a name="l00193"></a><span class="lineno"> 193</span> </div>
<div class="line"><a name="l00195"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#acecccc91c6a09c5814ee7f4923a53b3d"> 195</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#acecccc91c6a09c5814ee7f4923a53b3d">writeUserParam_</a>(std::ostream& os, <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MetaInfoInterface.html">MetaInfoInterface</a>& meta, <span class="keywordtype">int</span> indent = 4, <a class="code" href="classOpenMS_1_1String.html">String</a> tag = <span class="stringliteral">"nameValue"</span>)</div>
<div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  {</div>
<div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  std::vector<String> keys; <span class="comment">// Vector to hold keys to meta info</span></div>
<div class="line"><a name="l00198"></a><span class="lineno"> 198</span>  meta.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aaefa2a4a5d50f899cdd82d686104d164">getKeys</a>(keys);</div>
<div class="line"><a name="l00199"></a><span class="lineno"> 199</span> </div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span>  <span class="keywordflow">for</span> (std::vector<String>::const_iterator it = keys.begin(); it != keys.end(); ++it)</div>
<div class="line"><a name="l00201"></a><span class="lineno"> 201</span>  {</div>
<div class="line"><a name="l00202"></a><span class="lineno"> 202</span>  <span class="keywordflow">if</span> ((*it)[0] != <span class="charliteral">'#'</span>) <span class="comment">// internally used meta info start with '#'</span></div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  {</div>
<div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  os << <a class="code" href="classOpenMS_1_1String.html">String</a>(indent, <span class="charliteral">'\t'</span>) << <span class="stringliteral">"<"</span> << tag << <span class="stringliteral">" name=\""</span> << *it << <span class="stringliteral">"\" value=\""</span> << meta.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(*it) << <span class="stringliteral">"\"/>\n"</span>;</div>
<div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  }</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span>  }</div>
<div class="line"><a name="l00207"></a><span class="lineno"> 207</span>  }</div>
<div class="line"><a name="l00208"></a><span class="lineno"> 208</span> </div>
<div class="line"><a name="l00210"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a50a6b2cdb2828e1f3e29c0096fd4ef63"> 210</a></span>  std::vector<DataProcessing> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a50a6b2cdb2828e1f3e29c0096fd4ef63">data_processing_</a>;</div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span> </div>
<div class="line"><a name="l00212"></a><span class="lineno"> 212</span> <span class="keyword">private</span>:</div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a265fc94e4af4dab38234d47a0132342b">MzXMLHandler</a>();</div>
<div class="line"><a name="l00215"></a><span class="lineno"> 215</span> </div>
<div class="line"><a name="l00216"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a17154457c4614528cb46d566d022544b"> 216</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a17154457c4614528cb46d566d022544b">s_value_</a>;</div>
<div class="line"><a name="l00217"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae9e005976a3adc6ee08cc2d3dcfa3051"> 217</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae9e005976a3adc6ee08cc2d3dcfa3051">s_count_</a>;</div>
<div class="line"><a name="l00218"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a109ace998423bdd876eab260df9303a2"> 218</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a109ace998423bdd876eab260df9303a2">s_type_</a>;</div>
<div class="line"><a name="l00219"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5a8077778dc3c534832ee1a3d79e9e72"> 219</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5a8077778dc3c534832ee1a3d79e9e72">s_name_</a>;</div>
<div class="line"><a name="l00220"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5e48b11d87737bed51dd492038c41279"> 220</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5e48b11d87737bed51dd492038c41279">s_version_</a>;</div>
<div class="line"><a name="l00221"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5212e012d8c0950cb3070648f396f31a"> 221</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5212e012d8c0950cb3070648f396f31a">s_filename_</a>;</div>
<div class="line"><a name="l00222"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a65a51a09b69d61cd87bf7a27277e3aee"> 222</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a65a51a09b69d61cd87bf7a27277e3aee">s_filetype_</a>;</div>
<div class="line"><a name="l00223"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a00d2844792e6c6f7ad3fe2c46201a57a"> 223</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a00d2844792e6c6f7ad3fe2c46201a57a">s_filesha1_</a>;</div>
<div class="line"><a name="l00224"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ab4f6647bb6022332bcd7fbeadd0201b5"> 224</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ab4f6647bb6022332bcd7fbeadd0201b5">s_completiontime_</a>;</div>
<div class="line"><a name="l00225"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a390ecbd61eb171e0a00bff4616452d25"> 225</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a390ecbd61eb171e0a00bff4616452d25">s_precision_</a>;</div>
<div class="line"><a name="l00226"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4cd969d50e859e07ce2891b598a9a170"> 226</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4cd969d50e859e07ce2891b598a9a170">s_byteorder_</a>;</div>
<div class="line"><a name="l00227"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a7d4d4c968dc72284a6c9bfbdcde40b68"> 227</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a7d4d4c968dc72284a6c9bfbdcde40b68">s_pairorder_</a>;</div>
<div class="line"><a name="l00228"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a802a9eebc4a92192e11cd7aabec3d204"> 228</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a802a9eebc4a92192e11cd7aabec3d204">s_compressionType_</a>;</div>
<div class="line"><a name="l00229"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aa28e3da88956cfad247756b999df9abb"> 229</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aa28e3da88956cfad247756b999df9abb">s_precursorintensity_</a>;</div>
<div class="line"><a name="l00230"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a372aba127092cba03b2745c3bd71dcd2"> 230</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a372aba127092cba03b2745c3bd71dcd2">s_precursorcharge_</a>;</div>
<div class="line"><a name="l00231"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aafa58529452e61b34695d15a8fc44bc2"> 231</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aafa58529452e61b34695d15a8fc44bc2">s_windowwideness_</a>;</div>
<div class="line"><a name="l00232"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a0a4ccd2c235c704e0ade926b45f43302"> 232</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a0a4ccd2c235c704e0ade926b45f43302">s_mslevel_</a>;</div>
<div class="line"><a name="l00233"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a538550ae672ce0c5aa5a6e2b45688e9e"> 233</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a538550ae672ce0c5aa5a6e2b45688e9e">s_peakscount_</a>;</div>
<div class="line"><a name="l00234"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a9c58f650dc7adebf723a67fdf07e9b87"> 234</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a9c58f650dc7adebf723a67fdf07e9b87">s_polarity_</a>;</div>
<div class="line"><a name="l00235"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ad8f6ee9d6ad9dd9642c5f25864288ff0"> 235</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ad8f6ee9d6ad9dd9642c5f25864288ff0">s_scantype_</a>;</div>
<div class="line"><a name="l00236"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae58d7d4470df102db1bc01dfb2adaa07"> 236</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae58d7d4470df102db1bc01dfb2adaa07">s_retentiontime_</a>;</div>
<div class="line"><a name="l00237"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4ea3b391bd19b4cd96229423d1a1cf35"> 237</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4ea3b391bd19b4cd96229423d1a1cf35">s_startmz_</a>;</div>
<div class="line"><a name="l00238"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ad4338125b7a3027c186a41d554d63a74"> 238</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ad4338125b7a3027c186a41d554d63a74">s_endmz_</a>;</div>
<div class="line"><a name="l00239"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aa4a976a043fd323d6241a0e6a82274d9"> 239</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aa4a976a043fd323d6241a0e6a82274d9">s_first_</a>;</div>
<div class="line"><a name="l00240"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5a6d515dafa7fe4da638001e91bf1767"> 240</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5a6d515dafa7fe4da638001e91bf1767">s_last_</a>;</div>
<div class="line"><a name="l00241"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ac7f1dc19152ee580c397658d088a6a4f"> 241</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ac7f1dc19152ee580c397658d088a6a4f">s_phone_</a>;</div>
<div class="line"><a name="l00242"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a8554c50fb31c748b177745c43a06c595"> 242</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a8554c50fb31c748b177745c43a06c595">s_email_</a>;</div>
<div class="line"><a name="l00243"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a35ef4771d9814aae9cf44ba7feda927a"> 243</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a35ef4771d9814aae9cf44ba7feda927a">s_uri_</a>;</div>
<div class="line"><a name="l00244"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a6cc33a53f7b3712dd7102b572434d0cf"> 244</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a6cc33a53f7b3712dd7102b572434d0cf">s_num_</a>;</div>
<div class="line"><a name="l00245"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a38c21cb338ee0526513fdd9f8b701a59"> 245</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a38c21cb338ee0526513fdd9f8b701a59">s_intensitycutoff_</a>;</div>
<div class="line"><a name="l00246"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a3bcdda3510d6f4c85d3e3669fe044946"> 246</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a3bcdda3510d6f4c85d3e3669fe044946">s_centroided_</a>;</div>
<div class="line"><a name="l00247"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ac0db93030014443d6a620ac7459c1814"> 247</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ac0db93030014443d6a620ac7459c1814">s_deisotoped_</a>;</div>
<div class="line"><a name="l00248"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#adedd602ddb223d01302622fd5f5d3d5f"> 248</a></span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#adedd602ddb223d01302622fd5f5d3d5f">s_chargedeconvoluted_</a>;</div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span> </div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <span class="comment">// init all the static members, which is necessary because otherwise the undefined order will cause problems</span></div>
<div class="line"><a name="l00251"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a037915e92e9c138bbb22b3525420ad63"> 251</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a037915e92e9c138bbb22b3525420ad63">initStaticMembers_</a>()</div>
<div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  {</div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keyword">static</span> <span class="keywordtype">bool</span> init(<span class="keyword">false</span>);</div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  <span class="keywordflow">if</span> (!init)</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  {</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a17154457c4614528cb46d566d022544b">s_value_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"value"</span>);</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae9e005976a3adc6ee08cc2d3dcfa3051">s_count_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"scanCount"</span>);</div>
<div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a109ace998423bdd876eab260df9303a2">s_type_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"type"</span>);</div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5a8077778dc3c534832ee1a3d79e9e72">s_name_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"name"</span>);</div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5e48b11d87737bed51dd492038c41279">s_version_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"version"</span>);</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5212e012d8c0950cb3070648f396f31a">s_filename_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"fileName"</span>);</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a65a51a09b69d61cd87bf7a27277e3aee">s_filetype_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"fileType"</span>);</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a00d2844792e6c6f7ad3fe2c46201a57a">s_filesha1_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"fileSha1"</span>);</div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ab4f6647bb6022332bcd7fbeadd0201b5">s_completiontime_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"completionTime"</span>);</div>
<div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a390ecbd61eb171e0a00bff4616452d25">s_precision_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"precision"</span>);</div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4cd969d50e859e07ce2891b598a9a170">s_byteorder_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"byteOrder"</span>);</div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a7d4d4c968dc72284a6c9bfbdcde40b68">s_pairorder_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"pairOrder"</span>);</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a802a9eebc4a92192e11cd7aabec3d204">s_compressionType_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"compressionType"</span>);</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aa28e3da88956cfad247756b999df9abb">s_precursorintensity_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"precursorIntensity"</span>);</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a372aba127092cba03b2745c3bd71dcd2">s_precursorcharge_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"precursorCharge"</span>);</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aafa58529452e61b34695d15a8fc44bc2">s_windowwideness_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"windowWideness"</span>);</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a0a4ccd2c235c704e0ade926b45f43302">s_mslevel_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"msLevel"</span>);</div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a538550ae672ce0c5aa5a6e2b45688e9e">s_peakscount_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"peaksCount"</span>);</div>
<div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a9c58f650dc7adebf723a67fdf07e9b87">s_polarity_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"polarity"</span>);</div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ad8f6ee9d6ad9dd9642c5f25864288ff0">s_scantype_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"scanType"</span>);</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae58d7d4470df102db1bc01dfb2adaa07">s_retentiontime_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"retentionTime"</span>);</div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4ea3b391bd19b4cd96229423d1a1cf35">s_startmz_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"startMz"</span>);</div>
<div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ad4338125b7a3027c186a41d554d63a74">s_endmz_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"endMz"</span>);</div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aa4a976a043fd323d6241a0e6a82274d9">s_first_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"first"</span>);</div>
<div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5a6d515dafa7fe4da638001e91bf1767">s_last_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"last"</span>);</div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ac7f1dc19152ee580c397658d088a6a4f">s_phone_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"phone"</span>);</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a8554c50fb31c748b177745c43a06c595">s_email_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"email"</span>);</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a35ef4771d9814aae9cf44ba7feda927a">s_uri_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"URI"</span>);</div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a6cc33a53f7b3712dd7102b572434d0cf">s_num_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"num"</span>);</div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a38c21cb338ee0526513fdd9f8b701a59">s_intensitycutoff_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"intensityCutoff"</span>);</div>
<div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a3bcdda3510d6f4c85d3e3669fe044946">s_centroided_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"centroided"</span>);</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ac0db93030014443d6a620ac7459c1814">s_deisotoped_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"deisotoped"</span>);</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#adedd602ddb223d01302622fd5f5d3d5f">s_chargedeconvoluted_</a> = xercesc::XMLString::transcode(<span class="stringliteral">"chargeDeconvoluted"</span>);</div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span> </div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  init = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  }</div>
<div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  }</div>
<div class="line"><a name="l00294"></a><span class="lineno"> 294</span> </div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  };</div>
<div class="line"><a name="l00296"></a><span class="lineno"> 296</span> </div>
<div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  <span class="comment">//--------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00298"></a><span class="lineno"> 298</span> </div>
<div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  <span class="comment">// this cannot be moved into a function as VS2008 does not allow more than 31 static members in a function .. don't ask...</span></div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_value_</a> = 0;</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_count_</a> = 0;</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_type_</a> = 0;</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_name_</a> = 0;</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_version_</a> = 0;</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_filename_</a> = 0;</div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_filetype_</a> = 0;</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_filesha1_</a> = 0;</div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_completiontime_</a> = 0;</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_precision_</a> = 0;</div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_byteorder_</a> = 0;</div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_pairorder_</a> = 0;</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_compressionType_</a> = 0;</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_precursorintensity_</a> = 0;</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_precursorcharge_</a> = 0;</div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_windowwideness_</a> = 0;</div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_mslevel_</a> = 0;</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_peakscount_</a> = 0;</div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_polarity_</a> = 0;</div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_scantype_</a> = 0;</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_retentiontime_</a> = 0;</div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_startmz_</a> = 0;</div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_endmz_</a> = 0;</div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_first_</a> = 0;</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_last_</a> = 0;</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_phone_</a> = 0;</div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_email_</a> = 0;</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_uri_</a> = 0;</div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_num_</a> = 0;</div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_intensitycutoff_</a> = 0;</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_centroided_</a> = 0;</div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_deisotoped_</a> = 0;</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  <span class="keyword">const</span> XMLCh * <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">MzXMLHandler<MapType>::s_chargedeconvoluted_</a> = 0;</div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span> </div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00368"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aa1612242e2b5ea583324fadd8f0e5198"> 368</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aa1612242e2b5ea583324fadd8f0e5198">MzXMLHandler<MapType>::startElement</a>(<span class="keyword">const</span> XMLCh* <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> qname, <span class="keyword">const</span> xercesc::Attributes& attributes)</div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  {</div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <span class="keyword">static</span> <span class="keywordtype">bool</span> init_static_members(<span class="keyword">false</span>);</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  <span class="keywordflow">if</span> (!init_static_members)</div>
<div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  {</div>
<div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  initStaticMembers_();</div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  }</div>
<div class="line"><a name="l00375"></a><span class="lineno"> 375</span> </div>
<div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  <span class="keyword">static</span> <a class="code" href="classunsigned_01int.html">UInt</a> scan_count = 0;</div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span> </div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> tag = sm_.convert(qname);</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  open_tags_.push_back(tag);</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  <span class="comment">//std::cout << " -- Start -- "<< tag << " -- " << "\n";</span></div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span> </div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  <span class="comment">//Skip all tags until the the next scan</span></div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  <span class="keywordflow">if</span> (skip_spectrum_ && tag != <span class="stringliteral">"scan"</span>)</div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span> </div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  <span class="keywordflow">if</span> (tag == <span class="stringliteral">"msRun"</span>)</div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  {</div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> count = 0;</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  optionalAttributeAsInt_(count, attributes, s_count_);</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  exp_->reserve(count);</div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  logger_.startProgress(0, count, <span class="stringliteral">"loading mzXML file"</span>);</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  scan_count = 0;</div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  data_processing_.clear();</div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  <span class="comment">//start and end time are xs:duration. This makes no senes => ignore them</span></div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  }</div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"parentFile"</span>)</div>
<div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  {</div>
<div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  <a class="code" href="classOpenMS_1_1SourceFile.html">SourceFile</a> sf;</div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span>  sf.<a class="code" href="classOpenMS_1_1SourceFile.html#af0a7eddbacf20c4f4045b671df6b0fe7">setNameOfFile</a>(attributeAsString_(attributes, s_filename_));</div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  sf.<a class="code" href="classOpenMS_1_1SourceFile.html#a2d47bfad02d5ce05dcfab38bc1b21400">setFileType</a>(attributeAsString_(attributes, s_filetype_));</div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  sf.<a class="code" href="classOpenMS_1_1SourceFile.html#affa32793fdd4f1526a6c34c17626a60a">setChecksum</a>(attributeAsString_(attributes, s_filesha1_), <a class="code" href="classOpenMS_1_1SourceFile.html#a6440df7f4dbfc4c3370e2b6781bc74e5a27028cc8b5d6f0a1cb3030c180019abc">SourceFile::SHA1</a>);</div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  exp_->getSourceFiles().push_back(sf);</div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  }</div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"software"</span>)</div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  {</div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>& parent_tag = *(open_tags_.end() - 2);</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"dataProcessing"</span>)</div>
<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  {</div>
<div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  data_processing_.back().getSoftware().setVersion(attributeAsString_(attributes, s_version_));</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  data_processing_.back().getSoftware().setName(attributeAsString_(attributes, s_name_));</div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  data_processing_.back().setMetaValue(<span class="stringliteral">"#type"</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(attributeAsString_(attributes, s_type_)));</div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span> </div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> time;</div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  optionalAttributeAsString_(time, attributes, s_completiontime_);</div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  data_processing_.back().setCompletionTime(asDateTime_(time));</div>
<div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  }</div>
<div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"msInstrument"</span>)</div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  {</div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  exp_->getInstrument().getSoftware().setVersion(attributeAsString_(attributes, s_version_));</div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  exp_->getInstrument().getSoftware().setName(attributeAsString_(attributes, s_name_));</div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  }</div>
<div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  }</div>
<div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"peaks"</span>)</div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  {</div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  <span class="comment">//precision</span></div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  precision_ = <span class="stringliteral">"32"</span>;</div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  optionalAttributeAsString_(precision_, attributes, s_precision_);</div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  <span class="keywordflow">if</span> (precision_ != <span class="stringliteral">"32"</span> && precision_ != <span class="stringliteral">"64"</span>)</div>
<div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  {</div>
<div class="line"><a name="l00430"></a><span class="lineno"> 430</span>  error(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Invalid precision '"</span>) + precision_ + <span class="stringliteral">"' in element 'peaks'"</span>);</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  }</div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  <span class="comment">//byte order</span></div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> byte_order = <span class="stringliteral">"network"</span>;</div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  optionalAttributeAsString_(byte_order, attributes, s_byteorder_);</div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  <span class="keywordflow">if</span> (byte_order != <span class="stringliteral">"network"</span>)</div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  {</div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  error(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Invalid or missing byte order '"</span>) + byte_order + <span class="stringliteral">"' in element 'peaks'. Must be 'network'!"</span>);</div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  }</div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  <span class="comment">//pair order</span></div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> pair_order = <span class="stringliteral">"m/z-int"</span>;</div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  optionalAttributeAsString_(pair_order, attributes, s_pairorder_);</div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  <span class="keywordflow">if</span> (pair_order != <span class="stringliteral">"m/z-int"</span>)</div>
<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  {</div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  error(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Invalid or missing pair order '"</span>) + pair_order + <span class="stringliteral">"' in element 'peaks'. Must be 'm/z-int'!"</span>);</div>
<div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  }</div>
<div class="line"><a name="l00446"></a><span class="lineno"> 446</span>  <span class="comment">//compressionType</span></div>
<div class="line"><a name="l00447"></a><span class="lineno"> 447</span>  compressionType_ = <span class="stringliteral">"none"</span>;</div>
<div class="line"><a name="l00448"></a><span class="lineno"> 448</span>  optionalAttributeAsString_(compressionType_, attributes, s_compressionType_);</div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  <span class="keywordflow">if</span> (compressionType_ != <span class="stringliteral">"none"</span> && compressionType_ != <span class="stringliteral">"zlib"</span>)</div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  {</div>
<div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  error(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Invalid compression type "</span>) + compressionType_ + <span class="stringliteral">"in elements 'peaks'. Must be 'none' or 'zlib'! "</span>);</div>
<div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  }</div>
<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  }</div>
<div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"precursorMz"</span>)</div>
<div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  {</div>
<div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  <span class="comment">//add new precursor</span></div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  exp_->getSpectra().back().getPrecursors().push_back(<a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a>());</div>
<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  <span class="comment">//intensity</span></div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  {</div>
<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  exp_->getSpectra().back().getPrecursors().back().setIntensity(attributeAsDouble_(attributes, s_precursorintensity_));</div>
<div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  }</div>
<div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1ParseError.html">Exception::ParseError</a>& <span class="comment">/*e*/</span>)</div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  {</div>
<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  error(LOAD, <span class="stringliteral">"Mandatory attribute 'precursorIntensity' of tag 'precursorMz' not found! Setting precursor intensity to zero!"</span>);</div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  }</div>
<div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  <span class="comment">//charge</span></div>
<div class="line"><a name="l00468"></a><span class="lineno"> 468</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> charge = 0;</div>
<div class="line"><a name="l00469"></a><span class="lineno"> 469</span>  <span class="keywordflow">if</span> (optionalAttributeAsInt_(charge, attributes, s_precursorcharge_))</div>
<div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  {</div>
<div class="line"><a name="l00471"></a><span class="lineno"> 471</span>  exp_->getSpectra().back().getPrecursors().back().setCharge(charge);</div>
<div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  }</div>
<div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  <span class="comment">//window bounds (here only the width is stored in both fields - this is corrected when we parse the m/z position)</span></div>
<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  <a class="code" href="classdouble.html">DoubleReal</a> window = 0.0;</div>
<div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  <span class="keywordflow">if</span> (optionalAttributeAsDouble_(window, attributes, s_windowwideness_))</div>
<div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  {</div>
<div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  exp_->getSpectra().back().getPrecursors().back().setIsolationWindowLowerOffset(window);</div>
<div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  }</div>
<div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  }</div>
<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"scan"</span>)</div>
<div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  {</div>
<div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  skip_spectrum_ = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00483"></a><span class="lineno"> 483</span> </div>
<div class="line"><a name="l00484"></a><span class="lineno"> 484</span>  <span class="keywordflow">if</span> (options_.getMetadataOnly())</div>
<div class="line"><a name="l00485"></a><span class="lineno"> 485</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Internal_1_1XMLHandler_1_1EndParsingSoftly.html">EndParsingSoftly</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__);</div>
<div class="line"><a name="l00486"></a><span class="lineno"> 486</span> </div>
<div class="line"><a name="l00487"></a><span class="lineno"> 487</span>  <span class="comment">// check if the scan is in the desired MS / RT range</span></div>
<div class="line"><a name="l00488"></a><span class="lineno"> 488</span>  <a class="code" href="classunsigned_01int.html">UInt</a> ms_level = attributeAsInt_(attributes, s_mslevel_);</div>
<div class="line"><a name="l00489"></a><span class="lineno"> 489</span>  <span class="keywordflow">if</span> (ms_level == 0)</div>
<div class="line"><a name="l00490"></a><span class="lineno"> 490</span>  {</div>
<div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Invalid 'msLevel' attribute with value '0' in 'scan' element found. Assuming ms level 1!"</span>));</div>
<div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  ms_level = 1;</div>
<div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  }</div>
<div class="line"><a name="l00494"></a><span class="lineno"> 494</span> </div>
<div class="line"><a name="l00495"></a><span class="lineno"> 495</span>  <span class="comment">//parse retention time and convert it from xs:duration to seconds</span></div>
<div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  <a class="code" href="classdouble.html">DoubleReal</a> retention_time = 0.0;</div>
<div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> time_string = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00498"></a><span class="lineno"> 498</span>  <span class="keywordflow">if</span> (optionalAttributeAsString_(time_string, attributes, s_retentiontime_))</div>
<div class="line"><a name="l00499"></a><span class="lineno"> 499</span>  {</div>
<div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  time_string = time_string.<a class="code" href="classOpenMS_1_1String.html#a305141aabee4495bc55a45971af1f05e">suffix</a>(<span class="charliteral">'T'</span>);</div>
<div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  <span class="comment">//std::cout << "Initial trim: " << time_string << "\n";</span></div>
<div class="line"><a name="l00502"></a><span class="lineno"> 502</span>  <span class="keywordflow">if</span> (time_string.<a class="code" href="classOpenMS_1_1String.html#a58599d37159ebc08a654fb2d25be92fe">has</a>(<span class="charliteral">'H'</span>))</div>
<div class="line"><a name="l00503"></a><span class="lineno"> 503</span>  {</div>
<div class="line"><a name="l00504"></a><span class="lineno"> 504</span>  retention_time += 3600 * asDouble_(time_string.<a class="code" href="classOpenMS_1_1String.html#a3b68228d65702a6a614e8e4226d25b8d">prefix</a>(<span class="charliteral">'H'</span>));</div>
<div class="line"><a name="l00505"></a><span class="lineno"> 505</span>  time_string = time_string.<a class="code" href="classOpenMS_1_1String.html#a305141aabee4495bc55a45971af1f05e">suffix</a>(<span class="charliteral">'H'</span>);</div>
<div class="line"><a name="l00506"></a><span class="lineno"> 506</span>  <span class="comment">//std::cout << "After H: " << time_string << "\n";</span></div>
<div class="line"><a name="l00507"></a><span class="lineno"> 507</span>  }</div>
<div class="line"><a name="l00508"></a><span class="lineno"> 508</span>  <span class="keywordflow">if</span> (time_string.<a class="code" href="classOpenMS_1_1String.html#a58599d37159ebc08a654fb2d25be92fe">has</a>(<span class="charliteral">'M'</span>))</div>
<div class="line"><a name="l00509"></a><span class="lineno"> 509</span>  {</div>
<div class="line"><a name="l00510"></a><span class="lineno"> 510</span>  retention_time += 60 * asDouble_(time_string.<a class="code" href="classOpenMS_1_1String.html#a3b68228d65702a6a614e8e4226d25b8d">prefix</a>(<span class="charliteral">'M'</span>));</div>
<div class="line"><a name="l00511"></a><span class="lineno"> 511</span>  time_string = time_string.<a class="code" href="classOpenMS_1_1String.html#a305141aabee4495bc55a45971af1f05e">suffix</a>(<span class="charliteral">'M'</span>);</div>
<div class="line"><a name="l00512"></a><span class="lineno"> 512</span>  <span class="comment">//std::cout << "After M: " << time_string << "\n";</span></div>
<div class="line"><a name="l00513"></a><span class="lineno"> 513</span>  }</div>
<div class="line"><a name="l00514"></a><span class="lineno"> 514</span>  <span class="keywordflow">if</span> (time_string.<a class="code" href="classOpenMS_1_1String.html#a58599d37159ebc08a654fb2d25be92fe">has</a>(<span class="charliteral">'S'</span>))</div>
<div class="line"><a name="l00515"></a><span class="lineno"> 515</span>  {</div>
<div class="line"><a name="l00516"></a><span class="lineno"> 516</span>  retention_time += asDouble_(time_string.<a class="code" href="classOpenMS_1_1String.html#a3b68228d65702a6a614e8e4226d25b8d">prefix</a>(<span class="charliteral">'S'</span>));</div>
<div class="line"><a name="l00517"></a><span class="lineno"> 517</span>  time_string = time_string.<a class="code" href="classOpenMS_1_1String.html#a305141aabee4495bc55a45971af1f05e">suffix</a>(<span class="charliteral">'S'</span>);</div>
<div class="line"><a name="l00518"></a><span class="lineno"> 518</span>  <span class="comment">//std::cout << "After S: " << time_string << "\n";</span></div>
<div class="line"><a name="l00519"></a><span class="lineno"> 519</span>  }</div>
<div class="line"><a name="l00520"></a><span class="lineno"> 520</span>  }</div>
<div class="line"><a name="l00521"></a><span class="lineno"> 521</span> </div>
<div class="line"><a name="l00522"></a><span class="lineno"> 522</span>  logger_.setProgress(scan_count);</div>
<div class="line"><a name="l00523"></a><span class="lineno"> 523</span> </div>
<div class="line"><a name="l00524"></a><span class="lineno"> 524</span>  <span class="keywordflow">if</span> ((options_.hasRTRange() && !options_.getRTRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<1></a>(retention_time)))</div>
<div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  || (options_.hasMSLevels() && !options_.containsMSLevel(ms_level)))</div>
<div class="line"><a name="l00526"></a><span class="lineno"> 526</span>  {</div>
<div class="line"><a name="l00527"></a><span class="lineno"> 527</span>  <span class="comment">// skip this tag</span></div>
<div class="line"><a name="l00528"></a><span class="lineno"> 528</span>  skip_spectrum_ = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00529"></a><span class="lineno"> 529</span>  ++scan_count;</div>
<div class="line"><a name="l00530"></a><span class="lineno"> 530</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00531"></a><span class="lineno"> 531</span>  }</div>
<div class="line"><a name="l00532"></a><span class="lineno"> 532</span> </div>
<div class="line"><a name="l00533"></a><span class="lineno"> 533</span>  <span class="comment">//Add a new spectrum and set MS level and RT</span></div>
<div class="line"><a name="l00534"></a><span class="lineno"> 534</span>  exp_->resize(exp_->size() + 1);</div>
<div class="line"><a name="l00535"></a><span class="lineno"> 535</span>  exp_->getSpectra().back().setMSLevel(ms_level);</div>
<div class="line"><a name="l00536"></a><span class="lineno"> 536</span>  exp_->getSpectra().back().setRT(retention_time);</div>
<div class="line"><a name="l00537"></a><span class="lineno"> 537</span>  exp_->getSpectra().back().setNativeID(<a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"scan="</span>) + attributeAsString_(attributes, s_num_));</div>
<div class="line"><a name="l00538"></a><span class="lineno"> 538</span>  <span class="comment">//peak count == twice the scan size</span></div>
<div class="line"><a name="l00539"></a><span class="lineno"> 539</span>  peak_count_ = attributeAsInt_(attributes, s_peakscount_);</div>
<div class="line"><a name="l00540"></a><span class="lineno"> 540</span>  exp_->getSpectra().back().reserve(peak_count_ / 2 + 1);</div>
<div class="line"><a name="l00541"></a><span class="lineno"> 541</span>  exp_->getSpectra().back().setDataProcessing(data_processing_);</div>
<div class="line"><a name="l00542"></a><span class="lineno"> 542</span> </div>
<div class="line"><a name="l00543"></a><span class="lineno"> 543</span>  <span class="comment">//centroided, chargeDeconvoluted, deisotoped, collisionEnergy are ignored</span></div>
<div class="line"><a name="l00544"></a><span class="lineno"> 544</span> </div>
<div class="line"><a name="l00545"></a><span class="lineno"> 545</span>  <span class="comment">//other optional attributes</span></div>
<div class="line"><a name="l00546"></a><span class="lineno"> 546</span>  <a class="code" href="structOpenMS_1_1ScanWindow.html">ScanWindow</a> window;</div>
<div class="line"><a name="l00547"></a><span class="lineno"> 547</span>  optionalAttributeAsDouble_(window.<a class="code" href="structOpenMS_1_1ScanWindow.html#aea3ca80628c489842c52a61e195dd047">begin</a>, attributes, s_startmz_);</div>
<div class="line"><a name="l00548"></a><span class="lineno"> 548</span>  optionalAttributeAsDouble_(window.<a class="code" href="structOpenMS_1_1ScanWindow.html#aed18ab075b5c0317ae32335a57f899e8">end</a>, attributes, s_endmz_);</div>
<div class="line"><a name="l00549"></a><span class="lineno"> 549</span>  <span class="keywordflow">if</span> (window.<a class="code" href="structOpenMS_1_1ScanWindow.html#aea3ca80628c489842c52a61e195dd047">begin</a> != 0.0 || window.<a class="code" href="structOpenMS_1_1ScanWindow.html#aed18ab075b5c0317ae32335a57f899e8">end</a> != 0.0)</div>
<div class="line"><a name="l00550"></a><span class="lineno"> 550</span>  {</div>
<div class="line"><a name="l00551"></a><span class="lineno"> 551</span>  exp_->getSpectra().back().getInstrumentSettings().getScanWindows().push_back(window);</div>
<div class="line"><a name="l00552"></a><span class="lineno"> 552</span>  }</div>
<div class="line"><a name="l00553"></a><span class="lineno"> 553</span> </div>
<div class="line"><a name="l00554"></a><span class="lineno"> 554</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> polarity = <span class="stringliteral">"any"</span>;</div>
<div class="line"><a name="l00555"></a><span class="lineno"> 555</span>  optionalAttributeAsString_(polarity, attributes, s_polarity_);</div>
<div class="line"><a name="l00556"></a><span class="lineno"> 556</span>  exp_->getSpectra().back().getInstrumentSettings().setPolarity((<a class="code" href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054">IonSource::Polarity</a>) cvStringToEnum_(0, polarity, <span class="stringliteral">"polarity"</span>));</div>
<div class="line"><a name="l00557"></a><span class="lineno"> 557</span> </div>
<div class="line"><a name="l00558"></a><span class="lineno"> 558</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> type = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  optionalAttributeAsString_(type, attributes, s_scantype_);</div>
<div class="line"><a name="l00560"></a><span class="lineno"> 560</span>  <span class="keywordflow">if</span> (type == <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00561"></a><span class="lineno"> 561</span>  {</div>
<div class="line"><a name="l00562"></a><span class="lineno"> 562</span>  <span class="comment">//unknown/unset => do nothing here => no warning in the end</span></div>
<div class="line"><a name="l00563"></a><span class="lineno"> 563</span>  }</div>
<div class="line"><a name="l00564"></a><span class="lineno"> 564</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <span class="stringliteral">"zoom"</span>)</div>
<div class="line"><a name="l00565"></a><span class="lineno"> 565</span>  {</div>
<div class="line"><a name="l00566"></a><span class="lineno"> 566</span>  exp_->getSpectra().back().getInstrumentSettings().setZoomScan(<span class="keyword">true</span>);</div>
<div class="line"><a name="l00567"></a><span class="lineno"> 567</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l00568"></a><span class="lineno"> 568</span>  }</div>
<div class="line"><a name="l00569"></a><span class="lineno"> 569</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <span class="stringliteral">"Full"</span>)</div>
<div class="line"><a name="l00570"></a><span class="lineno"> 570</span>  {</div>
<div class="line"><a name="l00571"></a><span class="lineno"> 571</span>  <span class="keywordflow">if</span> (ms_level > 1)</div>
<div class="line"><a name="l00572"></a><span class="lineno"> 572</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad1561b04e39806321c10bc90516e846d">InstrumentSettings::MSNSPECTRUM</a>);</div>
<div class="line"><a name="l00573"></a><span class="lineno"> 573</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00574"></a><span class="lineno"> 574</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l00575"></a><span class="lineno"> 575</span>  }</div>
<div class="line"><a name="l00576"></a><span class="lineno"> 576</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <span class="stringliteral">"SIM"</span>)</div>
<div class="line"><a name="l00577"></a><span class="lineno"> 577</span>  {</div>
<div class="line"><a name="l00578"></a><span class="lineno"> 578</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746">InstrumentSettings::SIM</a>);</div>
<div class="line"><a name="l00579"></a><span class="lineno"> 579</span>  }</div>
<div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <span class="stringliteral">"SRM"</span> || type == <span class="stringliteral">"MRM"</span>)</div>
<div class="line"><a name="l00581"></a><span class="lineno"> 581</span>  {</div>
<div class="line"><a name="l00582"></a><span class="lineno"> 582</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">InstrumentSettings::SRM</a>);</div>
<div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  }</div>
<div class="line"><a name="l00584"></a><span class="lineno"> 584</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <span class="stringliteral">"CRM"</span>)</div>
<div class="line"><a name="l00585"></a><span class="lineno"> 585</span>  {</div>
<div class="line"><a name="l00586"></a><span class="lineno"> 586</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0af3d1715feea7314cc0ed1080191ea57d">InstrumentSettings::CRM</a>);</div>
<div class="line"><a name="l00587"></a><span class="lineno"> 587</span>  }</div>
<div class="line"><a name="l00588"></a><span class="lineno"> 588</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <span class="stringliteral">"Q1"</span>)</div>
<div class="line"><a name="l00589"></a><span class="lineno"> 589</span>  {</div>
<div class="line"><a name="l00590"></a><span class="lineno"> 590</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l00591"></a><span class="lineno"> 591</span>  }</div>
<div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <span class="stringliteral">"Q3"</span>)</div>
<div class="line"><a name="l00593"></a><span class="lineno"> 593</span>  {</div>
<div class="line"><a name="l00594"></a><span class="lineno"> 594</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l00595"></a><span class="lineno"> 595</span>  }</div>
<div class="line"><a name="l00596"></a><span class="lineno"> 596</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <span class="stringliteral">"EMS"</span>) <span class="comment">//Non-standard type: Enhanced MS (ABI - Sashimi converter)</span></div>
<div class="line"><a name="l00597"></a><span class="lineno"> 597</span>  {</div>
<div class="line"><a name="l00598"></a><span class="lineno"> 598</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l00599"></a><span class="lineno"> 599</span>  }</div>
<div class="line"><a name="l00600"></a><span class="lineno"> 600</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <span class="stringliteral">"EPI"</span>) <span class="comment">//Non-standard type: Enhanced Product Ion (ABI - Sashimi converter)</span></div>
<div class="line"><a name="l00601"></a><span class="lineno"> 601</span>  {</div>
<div class="line"><a name="l00602"></a><span class="lineno"> 602</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l00603"></a><span class="lineno"> 603</span>  exp_->getSpectra().back().setMSLevel(2);</div>
<div class="line"><a name="l00604"></a><span class="lineno"> 604</span>  }</div>
<div class="line"><a name="l00605"></a><span class="lineno"> 605</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (type == <span class="stringliteral">"ER"</span>) <span class="comment">// Non-standard type: Enhanced Resolution (ABI - Sashimi converter)</span></div>
<div class="line"><a name="l00606"></a><span class="lineno"> 606</span>  {</div>
<div class="line"><a name="l00607"></a><span class="lineno"> 607</span>  exp_->getSpectra().back().getInstrumentSettings().setZoomScan(<span class="keyword">true</span>);</div>
<div class="line"><a name="l00608"></a><span class="lineno"> 608</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l00609"></a><span class="lineno"> 609</span>  }</div>
<div class="line"><a name="l00610"></a><span class="lineno"> 610</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00611"></a><span class="lineno"> 611</span>  {</div>
<div class="line"><a name="l00612"></a><span class="lineno"> 612</span>  exp_->getSpectra().back().getInstrumentSettings().setScanMode(<a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>);</div>
<div class="line"><a name="l00613"></a><span class="lineno"> 613</span>  warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Unknown scan mode '"</span>) + type + <span class="stringliteral">"'. Assuming full scan"</span>);</div>
<div class="line"><a name="l00614"></a><span class="lineno"> 614</span>  }</div>
<div class="line"><a name="l00615"></a><span class="lineno"> 615</span> </div>
<div class="line"><a name="l00616"></a><span class="lineno"> 616</span>  ++scan_count;</div>
<div class="line"><a name="l00617"></a><span class="lineno"> 617</span>  }</div>
<div class="line"><a name="l00618"></a><span class="lineno"> 618</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"operator"</span>)</div>
<div class="line"><a name="l00619"></a><span class="lineno"> 619</span>  {</div>
<div class="line"><a name="l00620"></a><span class="lineno"> 620</span>  exp_->getContacts().resize(1);</div>
<div class="line"><a name="l00621"></a><span class="lineno"> 621</span>  exp_->getContacts().back().setFirstName(attributeAsString_(attributes, s_first_));</div>
<div class="line"><a name="l00622"></a><span class="lineno"> 622</span>  exp_->getContacts().back().setLastName(attributeAsString_(attributes, s_last_));</div>
<div class="line"><a name="l00623"></a><span class="lineno"> 623</span> </div>
<div class="line"><a name="l00624"></a><span class="lineno"> 624</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> tmp = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00625"></a><span class="lineno"> 625</span>  optionalAttributeAsString_(tmp, attributes, s_email_);</div>
<div class="line"><a name="l00626"></a><span class="lineno"> 626</span>  exp_->getContacts().back().setEmail(tmp);</div>
<div class="line"><a name="l00627"></a><span class="lineno"> 627</span> </div>
<div class="line"><a name="l00628"></a><span class="lineno"> 628</span>  tmp = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00629"></a><span class="lineno"> 629</span>  optionalAttributeAsString_(tmp, attributes, s_phone_);</div>
<div class="line"><a name="l00630"></a><span class="lineno"> 630</span>  <span class="keywordflow">if</span> (tmp != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00631"></a><span class="lineno"> 631</span>  {</div>
<div class="line"><a name="l00632"></a><span class="lineno"> 632</span>  exp_->getContacts().back().setMetaValue(<span class="stringliteral">"#phone"</span>, tmp);</div>
<div class="line"><a name="l00633"></a><span class="lineno"> 633</span>  }</div>
<div class="line"><a name="l00634"></a><span class="lineno"> 634</span> </div>
<div class="line"><a name="l00635"></a><span class="lineno"> 635</span>  tmp = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00636"></a><span class="lineno"> 636</span>  optionalAttributeAsString_(tmp, attributes, s_uri_);</div>
<div class="line"><a name="l00637"></a><span class="lineno"> 637</span>  exp_->getContacts().back().setURL(tmp);</div>
<div class="line"><a name="l00638"></a><span class="lineno"> 638</span>  }</div>
<div class="line"><a name="l00639"></a><span class="lineno"> 639</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"msManufacturer"</span>)</div>
<div class="line"><a name="l00640"></a><span class="lineno"> 640</span>  {</div>
<div class="line"><a name="l00641"></a><span class="lineno"> 641</span>  exp_->getInstrument().setVendor(attributeAsString_(attributes, s_value_));</div>
<div class="line"><a name="l00642"></a><span class="lineno"> 642</span>  }</div>
<div class="line"><a name="l00643"></a><span class="lineno"> 643</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"msModel"</span>)</div>
<div class="line"><a name="l00644"></a><span class="lineno"> 644</span>  {</div>
<div class="line"><a name="l00645"></a><span class="lineno"> 645</span>  exp_->getInstrument().setModel(attributeAsString_(attributes, s_value_));</div>
<div class="line"><a name="l00646"></a><span class="lineno"> 646</span>  }</div>
<div class="line"><a name="l00647"></a><span class="lineno"> 647</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"msIonisation"</span>)</div>
<div class="line"><a name="l00648"></a><span class="lineno"> 648</span>  {</div>
<div class="line"><a name="l00649"></a><span class="lineno"> 649</span>  exp_->getInstrument().getIonSources().resize(1);</div>
<div class="line"><a name="l00650"></a><span class="lineno"> 650</span>  exp_->getInstrument().getIonSources()[0].setIonizationMethod((<a class="code" href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4">IonSource::IonizationMethod</a>) cvStringToEnum_(2, attributeAsString_(attributes, s_value_), <span class="stringliteral">"msIonization"</span>));</div>
<div class="line"><a name="l00651"></a><span class="lineno"> 651</span>  }</div>
<div class="line"><a name="l00652"></a><span class="lineno"> 652</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"msMassAnalyzer"</span>)</div>
<div class="line"><a name="l00653"></a><span class="lineno"> 653</span>  {</div>
<div class="line"><a name="l00654"></a><span class="lineno"> 654</span>  exp_->getInstrument().getMassAnalyzers().resize(1);</div>
<div class="line"><a name="l00655"></a><span class="lineno"> 655</span>  exp_->getInstrument().getMassAnalyzers()[0].setType((<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3">MassAnalyzer::AnalyzerType</a>) cvStringToEnum_(3, attributeAsString_(attributes, s_value_), <span class="stringliteral">"msMassAnalyzer"</span>));</div>
<div class="line"><a name="l00656"></a><span class="lineno"> 656</span>  }</div>
<div class="line"><a name="l00657"></a><span class="lineno"> 657</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"msDetector"</span>)</div>
<div class="line"><a name="l00658"></a><span class="lineno"> 658</span>  {</div>
<div class="line"><a name="l00659"></a><span class="lineno"> 659</span>  exp_->getInstrument().getIonDetectors().resize(1);</div>
<div class="line"><a name="l00660"></a><span class="lineno"> 660</span>  exp_->getInstrument().getIonDetectors()[0].setType((<a class="code" href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7">IonDetector::Type</a>) cvStringToEnum_(4, attributeAsString_(attributes, s_value_), <span class="stringliteral">"msDetector"</span>));</div>
<div class="line"><a name="l00661"></a><span class="lineno"> 661</span>  }</div>
<div class="line"><a name="l00662"></a><span class="lineno"> 662</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"msResolution"</span>)</div>
<div class="line"><a name="l00663"></a><span class="lineno"> 663</span>  {</div>
<div class="line"><a name="l00664"></a><span class="lineno"> 664</span>  exp_->getInstrument().getMassAnalyzers()[0].setResolutionMethod((<a class="code" href="classOpenMS_1_1MassAnalyzer.html#a11053909f1f8edf7b9ccc41c1417ecf6">MassAnalyzer::ResolutionMethod</a>) cvStringToEnum_(5, attributeAsString_(attributes, s_value_), <span class="stringliteral">"msResolution"</span>));</div>
<div class="line"><a name="l00665"></a><span class="lineno"> 665</span>  }</div>
<div class="line"><a name="l00666"></a><span class="lineno"> 666</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"dataProcessing"</span>)</div>
<div class="line"><a name="l00667"></a><span class="lineno"> 667</span>  {</div>
<div class="line"><a name="l00668"></a><span class="lineno"> 668</span>  data_processing_.push_back(<a class="code" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a>());</div>
<div class="line"><a name="l00669"></a><span class="lineno"> 669</span> </div>
<div class="line"><a name="l00670"></a><span class="lineno"> 670</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> <span class="keywordtype">boolean</span> = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00671"></a><span class="lineno"> 671</span>  optionalAttributeAsString_(<span class="keywordtype">boolean</span>, attributes, s_deisotoped_);</div>
<div class="line"><a name="l00672"></a><span class="lineno"> 672</span>  <span class="keywordflow">if</span> (<span class="keywordtype">boolean</span> == <span class="stringliteral">"true"</span> || <span class="keywordtype">boolean</span> == <span class="stringliteral">"1"</span>)</div>
<div class="line"><a name="l00673"></a><span class="lineno"> 673</span>  {</div>
<div class="line"><a name="l00674"></a><span class="lineno"> 674</span>  data_processing_.back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a1491834ae41afad2cd5d4e69f20aaaae">DataProcessing::DEISOTOPING</a>);</div>
<div class="line"><a name="l00675"></a><span class="lineno"> 675</span>  }</div>
<div class="line"><a name="l00676"></a><span class="lineno"> 676</span> </div>
<div class="line"><a name="l00677"></a><span class="lineno"> 677</span>  <span class="keywordtype">boolean</span> = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00678"></a><span class="lineno"> 678</span>  optionalAttributeAsString_(<span class="keywordtype">boolean</span>, attributes, s_chargedeconvoluted_);</div>
<div class="line"><a name="l00679"></a><span class="lineno"> 679</span>  <span class="keywordflow">if</span> (<span class="keywordtype">boolean</span> == <span class="stringliteral">"true"</span> || <span class="keywordtype">boolean</span> == <span class="stringliteral">"1"</span>)</div>
<div class="line"><a name="l00680"></a><span class="lineno"> 680</span>  {</div>
<div class="line"><a name="l00681"></a><span class="lineno"> 681</span>  data_processing_.back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ad6aaf5187119b5738f4648dcb932c240">DataProcessing::CHARGE_DECONVOLUTION</a>);</div>
<div class="line"><a name="l00682"></a><span class="lineno"> 682</span>  }</div>
<div class="line"><a name="l00683"></a><span class="lineno"> 683</span> </div>
<div class="line"><a name="l00684"></a><span class="lineno"> 684</span>  <a class="code" href="classdouble.html">DoubleReal</a> cutoff = 0.0;</div>
<div class="line"><a name="l00685"></a><span class="lineno"> 685</span>  optionalAttributeAsDouble_(cutoff, attributes, s_intensitycutoff_);</div>
<div class="line"><a name="l00686"></a><span class="lineno"> 686</span>  <span class="keywordflow">if</span> (cutoff != 0.0)</div>
<div class="line"><a name="l00687"></a><span class="lineno"> 687</span>  {</div>
<div class="line"><a name="l00688"></a><span class="lineno"> 688</span>  data_processing_.back().setMetaValue(<span class="stringliteral">"#intensity_cutoff"</span>, cutoff);</div>
<div class="line"><a name="l00689"></a><span class="lineno"> 689</span>  }</div>
<div class="line"><a name="l00690"></a><span class="lineno"> 690</span> </div>
<div class="line"><a name="l00691"></a><span class="lineno"> 691</span>  <span class="keywordtype">boolean</span> = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00692"></a><span class="lineno"> 692</span>  optionalAttributeAsString_(<span class="keywordtype">boolean</span>, attributes, s_centroided_);</div>
<div class="line"><a name="l00693"></a><span class="lineno"> 693</span>  <span class="keywordflow">if</span> (<span class="keywordtype">boolean</span> == <span class="stringliteral">"true"</span> || <span class="keywordtype">boolean</span> == <span class="stringliteral">"1"</span>)</div>
<div class="line"><a name="l00694"></a><span class="lineno"> 694</span>  {</div>
<div class="line"><a name="l00695"></a><span class="lineno"> 695</span>  data_processing_.back().getProcessingActions().insert(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a181a4b8e81bcfae30e38dc548a5586f3">DataProcessing::PEAK_PICKING</a>);</div>
<div class="line"><a name="l00696"></a><span class="lineno"> 696</span>  }</div>
<div class="line"><a name="l00697"></a><span class="lineno"> 697</span>  }</div>
<div class="line"><a name="l00698"></a><span class="lineno"> 698</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"nameValue"</span>)</div>
<div class="line"><a name="l00699"></a><span class="lineno"> 699</span>  {</div>
<div class="line"><a name="l00700"></a><span class="lineno"> 700</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> name = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00701"></a><span class="lineno"> 701</span>  optionalAttributeAsString_(name, attributes, s_name_);</div>
<div class="line"><a name="l00702"></a><span class="lineno"> 702</span>  <span class="keywordflow">if</span> (name == <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00703"></a><span class="lineno"> 703</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00704"></a><span class="lineno"> 704</span> </div>
<div class="line"><a name="l00705"></a><span class="lineno"> 705</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> value = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00706"></a><span class="lineno"> 706</span>  optionalAttributeAsString_(value, attributes, s_value_);</div>
<div class="line"><a name="l00707"></a><span class="lineno"> 707</span> </div>
<div class="line"><a name="l00708"></a><span class="lineno"> 708</span>  <a class="code" href="classOpenMS_1_1String.html">String</a>& parent_tag = *(open_tags_.end() - 2);</div>
<div class="line"><a name="l00709"></a><span class="lineno"> 709</span> </div>
<div class="line"><a name="l00710"></a><span class="lineno"> 710</span>  <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"msInstrument"</span>)</div>
<div class="line"><a name="l00711"></a><span class="lineno"> 711</span>  {</div>
<div class="line"><a name="l00712"></a><span class="lineno"> 712</span>  exp_->getInstrument().setMetaValue(name, value);</div>
<div class="line"><a name="l00713"></a><span class="lineno"> 713</span>  }</div>
<div class="line"><a name="l00714"></a><span class="lineno"> 714</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"scan"</span>)</div>
<div class="line"><a name="l00715"></a><span class="lineno"> 715</span>  {</div>
<div class="line"><a name="l00716"></a><span class="lineno"> 716</span>  exp_->getSpectra().back().setMetaValue(name, value);</div>
<div class="line"><a name="l00717"></a><span class="lineno"> 717</span>  }</div>
<div class="line"><a name="l00718"></a><span class="lineno"> 718</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00719"></a><span class="lineno"> 719</span>  {</div>
<div class="line"><a name="l00720"></a><span class="lineno"> 720</span>  std::cout << <span class="stringliteral">" Warning: Unexpected tag 'nameValue' in tag '"</span> << parent_tag << <span class="stringliteral">"'"</span> << <span class="stringliteral">"\n"</span>;</div>
<div class="line"><a name="l00721"></a><span class="lineno"> 721</span>  }</div>
<div class="line"><a name="l00722"></a><span class="lineno"> 722</span>  }</div>
<div class="line"><a name="l00723"></a><span class="lineno"> 723</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (tag == <span class="stringliteral">"processingOperation"</span>)</div>
<div class="line"><a name="l00724"></a><span class="lineno"> 724</span>  {</div>
<div class="line"><a name="l00725"></a><span class="lineno"> 725</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> name = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00726"></a><span class="lineno"> 726</span>  optionalAttributeAsString_(name, attributes, s_name_);</div>
<div class="line"><a name="l00727"></a><span class="lineno"> 727</span>  <span class="keywordflow">if</span> (name == <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00728"></a><span class="lineno"> 728</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00729"></a><span class="lineno"> 729</span> </div>
<div class="line"><a name="l00730"></a><span class="lineno"> 730</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> value = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00731"></a><span class="lineno"> 731</span>  optionalAttributeAsString_(value, attributes, s_value_);</div>
<div class="line"><a name="l00732"></a><span class="lineno"> 732</span> </div>
<div class="line"><a name="l00733"></a><span class="lineno"> 733</span>  data_processing_.back().setMetaValue(name, value);</div>
<div class="line"><a name="l00734"></a><span class="lineno"> 734</span>  }</div>
<div class="line"><a name="l00735"></a><span class="lineno"> 735</span> </div>
<div class="line"><a name="l00736"></a><span class="lineno"> 736</span>  <span class="comment">//std::cout << " -- !Start -- " << "\n";</span></div>
<div class="line"><a name="l00737"></a><span class="lineno"> 737</span>  }</div>
<div class="line"><a name="l00738"></a><span class="lineno"> 738</span> </div>
<div class="line"><a name="l00739"></a><span class="lineno"> 739</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00740"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a8df65a3d6767516b62d0e4c84a14a4f4"> 740</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a8df65a3d6767516b62d0e4c84a14a4f4">MzXMLHandler<MapType>::endElement</a>(<span class="keyword">const</span> XMLCh* <span class="keyword">const</span> <span class="comment">/*uri*/</span>, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> <span class="comment">/*local_name*/</span>, <span class="keyword">const</span> XMLCh* <span class="keyword">const</span> qname)</div>
<div class="line"><a name="l00741"></a><span class="lineno"> 741</span>  {</div>
<div class="line"><a name="l00742"></a><span class="lineno"> 742</span>  <span class="comment">//std::cout << " -- End -- " << sm_.convert(qname) << " -- " << "\n";</span></div>
<div class="line"><a name="l00743"></a><span class="lineno"> 743</span> </div>
<div class="line"><a name="l00744"></a><span class="lineno"> 744</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_mzxml = xercesc::XMLString::transcode(<span class="stringliteral">"mzXML"</span>);</div>
<div class="line"><a name="l00745"></a><span class="lineno"> 745</span>  <span class="keyword">static</span> <span class="keyword">const</span> XMLCh* s_peaks = xercesc::XMLString::transcode(<span class="stringliteral">"peaks"</span>);</div>
<div class="line"><a name="l00746"></a><span class="lineno"> 746</span> </div>
<div class="line"><a name="l00747"></a><span class="lineno"> 747</span>  open_tags_.pop_back();</div>
<div class="line"><a name="l00748"></a><span class="lineno"> 748</span> </div>
<div class="line"><a name="l00749"></a><span class="lineno"> 749</span>  <span class="comment">//abort if this scan should be skipped</span></div>
<div class="line"><a name="l00750"></a><span class="lineno"> 750</span>  <span class="keywordflow">if</span> (skip_spectrum_)</div>
<div class="line"><a name="l00751"></a><span class="lineno"> 751</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00752"></a><span class="lineno"> 752</span> </div>
<div class="line"><a name="l00753"></a><span class="lineno"> 753</span>  <span class="keywordflow">if</span> (equal_(qname, s_mzxml))</div>
<div class="line"><a name="l00754"></a><span class="lineno"> 754</span>  {</div>
<div class="line"><a name="l00755"></a><span class="lineno"> 755</span>  logger_.endProgress();</div>
<div class="line"><a name="l00756"></a><span class="lineno"> 756</span>  }</div>
<div class="line"><a name="l00757"></a><span class="lineno"> 757</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (equal_(qname, s_peaks))</div>
<div class="line"><a name="l00758"></a><span class="lineno"> 758</span>  {</div>
<div class="line"><a name="l00759"></a><span class="lineno"> 759</span>  <span class="comment">//std::cout << "reading scan" << "\n";</span></div>
<div class="line"><a name="l00760"></a><span class="lineno"> 760</span>  <span class="keywordflow">if</span> (char_rest_ == <span class="stringliteral">""</span>) <span class="comment">// no peaks</span></div>
<div class="line"><a name="l00761"></a><span class="lineno"> 761</span>  {</div>
<div class="line"><a name="l00762"></a><span class="lineno"> 762</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00763"></a><span class="lineno"> 763</span>  }</div>
<div class="line"><a name="l00764"></a><span class="lineno"> 764</span> </div>
<div class="line"><a name="l00765"></a><span class="lineno"> 765</span>  <span class="comment">//remove whitespaces from binary data</span></div>
<div class="line"><a name="l00766"></a><span class="lineno"> 766</span>  <span class="comment">//this should not be necessary, but linebreaks inside the base64 data are unfortunately no exception</span></div>
<div class="line"><a name="l00767"></a><span class="lineno"> 767</span>  char_rest_.removeWhitespaces();</div>
<div class="line"><a name="l00768"></a><span class="lineno"> 768</span> </div>
<div class="line"><a name="l00769"></a><span class="lineno"> 769</span>  <span class="keywordflow">if</span> (precision_ == <span class="stringliteral">"64"</span>)</div>
<div class="line"><a name="l00770"></a><span class="lineno"> 770</span>  {</div>
<div class="line"><a name="l00771"></a><span class="lineno"> 771</span>  std::vector<DoubleReal> data;</div>
<div class="line"><a name="l00772"></a><span class="lineno"> 772</span>  <span class="keywordflow">if</span> (compressionType_ == <span class="stringliteral">"zlib"</span>)</div>
<div class="line"><a name="l00773"></a><span class="lineno"> 773</span>  {</div>
<div class="line"><a name="l00774"></a><span class="lineno"> 774</span>  decoder_.decode(char_rest_, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142ba6e7bcd2266b848fe3284e93c291c42b4">Base64::BYTEORDER_BIGENDIAN</a>, data, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00775"></a><span class="lineno"> 775</span>  }</div>
<div class="line"><a name="l00776"></a><span class="lineno"> 776</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00777"></a><span class="lineno"> 777</span>  {</div>
<div class="line"><a name="l00778"></a><span class="lineno"> 778</span>  decoder_.decode(char_rest_, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142ba6e7bcd2266b848fe3284e93c291c42b4">Base64::BYTEORDER_BIGENDIAN</a>, data);</div>
<div class="line"><a name="l00779"></a><span class="lineno"> 779</span>  }</div>
<div class="line"><a name="l00780"></a><span class="lineno"> 780</span>  char_rest_ = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00781"></a><span class="lineno"> 781</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884">PeakType</a> peak;</div>
<div class="line"><a name="l00782"></a><span class="lineno"> 782</span>  <span class="comment">//push_back the peaks into the container</span></div>
<div class="line"><a name="l00783"></a><span class="lineno"> 783</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n = 0; n < (2 * peak_count_); n += 2)</div>
<div class="line"><a name="l00784"></a><span class="lineno"> 784</span>  {</div>
<div class="line"><a name="l00785"></a><span class="lineno"> 785</span>  <span class="comment">// check if peak in in the specified m/z and intensity range</span></div>
<div class="line"><a name="l00786"></a><span class="lineno"> 786</span>  <span class="keywordflow">if</span> ((!options_.hasMZRange() || options_.getMZRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<1></a>(data[n])))</div>
<div class="line"><a name="l00787"></a><span class="lineno"> 787</span>  && (!options_.hasIntensityRange() || options_.getIntensityRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<1></a>(data[n + 1]))))</div>
<div class="line"><a name="l00788"></a><span class="lineno"> 788</span>  {</div>
<div class="line"><a name="l00789"></a><span class="lineno"> 789</span>  peak.setMZ(data[n]);</div>
<div class="line"><a name="l00790"></a><span class="lineno"> 790</span>  peak.setIntensity(data[n + 1]);</div>
<div class="line"><a name="l00791"></a><span class="lineno"> 791</span>  exp_->getSpectra().back().push_back(peak);</div>
<div class="line"><a name="l00792"></a><span class="lineno"> 792</span>  }</div>
<div class="line"><a name="l00793"></a><span class="lineno"> 793</span>  }</div>
<div class="line"><a name="l00794"></a><span class="lineno"> 794</span>  }</div>
<div class="line"><a name="l00795"></a><span class="lineno"> 795</span>  <span class="keywordflow">else</span> <span class="comment">//precision 32</span></div>
<div class="line"><a name="l00796"></a><span class="lineno"> 796</span>  {</div>
<div class="line"><a name="l00797"></a><span class="lineno"> 797</span>  std::vector<Real> data;</div>
<div class="line"><a name="l00798"></a><span class="lineno"> 798</span>  <span class="keywordflow">if</span> (compressionType_ == <span class="stringliteral">"zlib"</span>)</div>
<div class="line"><a name="l00799"></a><span class="lineno"> 799</span>  {</div>
<div class="line"><a name="l00800"></a><span class="lineno"> 800</span>  decoder_.decode(char_rest_, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142ba6e7bcd2266b848fe3284e93c291c42b4">Base64::BYTEORDER_BIGENDIAN</a>, data, <span class="keyword">true</span>);</div>
<div class="line"><a name="l00801"></a><span class="lineno"> 801</span>  }</div>
<div class="line"><a name="l00802"></a><span class="lineno"> 802</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00803"></a><span class="lineno"> 803</span>  {</div>
<div class="line"><a name="l00804"></a><span class="lineno"> 804</span>  decoder_.decode(char_rest_, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142ba6e7bcd2266b848fe3284e93c291c42b4">Base64::BYTEORDER_BIGENDIAN</a>, data);</div>
<div class="line"><a name="l00805"></a><span class="lineno"> 805</span>  }</div>
<div class="line"><a name="l00806"></a><span class="lineno"> 806</span>  char_rest_ = <span class="stringliteral">""</span>;</div>
<div class="line"><a name="l00807"></a><span class="lineno"> 807</span>  <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884">PeakType</a> peak;</div>
<div class="line"><a name="l00808"></a><span class="lineno"> 808</span>  <span class="comment">//push_back the peaks into the container</span></div>
<div class="line"><a name="l00809"></a><span class="lineno"> 809</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> n = 0; n < (2 * peak_count_); n += 2)</div>
<div class="line"><a name="l00810"></a><span class="lineno"> 810</span>  {</div>
<div class="line"><a name="l00811"></a><span class="lineno"> 811</span>  <span class="keywordflow">if</span> ((!options_.hasMZRange() || options_.getMZRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<1></a>(data[n])))</div>
<div class="line"><a name="l00812"></a><span class="lineno"> 812</span>  && (!options_.hasIntensityRange() || options_.getIntensityRange().encloses(<a class="code" href="classOpenMS_1_1DPosition.html">DPosition<1></a>(data[n + 1]))))</div>
<div class="line"><a name="l00813"></a><span class="lineno"> 813</span>  {</div>
<div class="line"><a name="l00814"></a><span class="lineno"> 814</span>  peak.setMZ(data[n]);</div>
<div class="line"><a name="l00815"></a><span class="lineno"> 815</span>  peak.setIntensity(data[n + 1]);</div>
<div class="line"><a name="l00816"></a><span class="lineno"> 816</span>  exp_->getSpectra().back().push_back(peak);</div>
<div class="line"><a name="l00817"></a><span class="lineno"> 817</span>  }</div>
<div class="line"><a name="l00818"></a><span class="lineno"> 818</span>  }</div>
<div class="line"><a name="l00819"></a><span class="lineno"> 819</span>  }</div>
<div class="line"><a name="l00820"></a><span class="lineno"> 820</span>  }</div>
<div class="line"><a name="l00821"></a><span class="lineno"> 821</span>  <span class="comment">//std::cout << " -- End -- " << "\n";</span></div>
<div class="line"><a name="l00822"></a><span class="lineno"> 822</span>  sm_.clear();</div>
<div class="line"><a name="l00823"></a><span class="lineno"> 823</span>  }</div>
<div class="line"><a name="l00824"></a><span class="lineno"> 824</span> </div>
<div class="line"><a name="l00825"></a><span class="lineno"> 825</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00826"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a742bdba7e6348fe6c549aada2a116944"> 826</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a742bdba7e6348fe6c549aada2a116944">MzXMLHandler<MapType>::characters</a>(<span class="keyword">const</span> XMLCh* <span class="keyword">const</span> chars, <span class="keyword">const</span> XMLSize_t <span class="comment">/*length*/</span>)</div>
<div class="line"><a name="l00827"></a><span class="lineno"> 827</span>  {</div>
<div class="line"><a name="l00828"></a><span class="lineno"> 828</span>  <span class="comment">//Abort if this spectrum should be skipped</span></div>
<div class="line"><a name="l00829"></a><span class="lineno"> 829</span>  <span class="keywordflow">if</span> (skip_spectrum_)</div>
<div class="line"><a name="l00830"></a><span class="lineno"> 830</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00831"></a><span class="lineno"> 831</span> </div>
<div class="line"><a name="l00832"></a><span class="lineno"> 832</span>  <span class="keywordtype">char</span>* transcoded_chars = sm_.convert(chars);</div>
<div class="line"><a name="l00833"></a><span class="lineno"> 833</span> </div>
<div class="line"><a name="l00834"></a><span class="lineno"> 834</span>  <span class="keywordflow">if</span> (open_tags_.back() == <span class="stringliteral">"peaks"</span>)</div>
<div class="line"><a name="l00835"></a><span class="lineno"> 835</span>  {</div>
<div class="line"><a name="l00836"></a><span class="lineno"> 836</span>  <span class="comment">//chars may be split to several chunks => concatenate them</span></div>
<div class="line"><a name="l00837"></a><span class="lineno"> 837</span>  char_rest_ += transcoded_chars;</div>
<div class="line"><a name="l00838"></a><span class="lineno"> 838</span>  }</div>
<div class="line"><a name="l00839"></a><span class="lineno"> 839</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (open_tags_.back() == <span class="stringliteral">"offset"</span> || open_tags_.back() == <span class="stringliteral">"indexOffset"</span> || open_tags_.back() == <span class="stringliteral">"sha1"</span>)</div>
<div class="line"><a name="l00840"></a><span class="lineno"> 840</span>  {</div>
<div class="line"><a name="l00841"></a><span class="lineno"> 841</span> </div>
<div class="line"><a name="l00842"></a><span class="lineno"> 842</span>  }</div>
<div class="line"><a name="l00843"></a><span class="lineno"> 843</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (open_tags_.back() == <span class="stringliteral">"precursorMz"</span>)</div>
<div class="line"><a name="l00844"></a><span class="lineno"> 844</span>  {</div>
<div class="line"><a name="l00845"></a><span class="lineno"> 845</span>  <a class="code" href="classdouble.html">DoubleReal</a> mz_pos = asDouble_(transcoded_chars);</div>
<div class="line"><a name="l00846"></a><span class="lineno"> 846</span>  <span class="comment">//precursor m/z</span></div>
<div class="line"><a name="l00847"></a><span class="lineno"> 847</span>  exp_->getSpectra().back().getPrecursors().back().setMZ(mz_pos);</div>
<div class="line"><a name="l00848"></a><span class="lineno"> 848</span>  <span class="comment">//update window bounds - center them around the m/z pos</span></div>
<div class="line"><a name="l00849"></a><span class="lineno"> 849</span>  <a class="code" href="classdouble.html">DoubleReal</a> window_width = exp_->getSpectra().back().getPrecursors().back().getIsolationWindowLowerOffset();</div>
<div class="line"><a name="l00850"></a><span class="lineno"> 850</span>  <span class="keywordflow">if</span> (window_width != 0.0)</div>
<div class="line"><a name="l00851"></a><span class="lineno"> 851</span>  {</div>
<div class="line"><a name="l00852"></a><span class="lineno"> 852</span>  exp_->getSpectra().back().getPrecursors().back().setIsolationWindowLowerOffset(mz_pos - 0.5 * window_width);</div>
<div class="line"><a name="l00853"></a><span class="lineno"> 853</span>  exp_->getSpectra().back().getPrecursors().back().setIsolationWindowUpperOffset(mz_pos + 0.5 * window_width);</div>
<div class="line"><a name="l00854"></a><span class="lineno"> 854</span>  }</div>
<div class="line"><a name="l00855"></a><span class="lineno"> 855</span>  }</div>
<div class="line"><a name="l00856"></a><span class="lineno"> 856</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (open_tags_.back() == <span class="stringliteral">"comment"</span>)</div>
<div class="line"><a name="l00857"></a><span class="lineno"> 857</span>  {</div>
<div class="line"><a name="l00858"></a><span class="lineno"> 858</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> parent_tag = *(open_tags_.end() - 2);</div>
<div class="line"><a name="l00859"></a><span class="lineno"> 859</span>  <span class="comment">//std::cout << "- Comment of parent " << parent_tag << "\n";</span></div>
<div class="line"><a name="l00860"></a><span class="lineno"> 860</span> </div>
<div class="line"><a name="l00861"></a><span class="lineno"> 861</span>  <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"msInstrument"</span>)</div>
<div class="line"><a name="l00862"></a><span class="lineno"> 862</span>  {</div>
<div class="line"><a name="l00863"></a><span class="lineno"> 863</span>  exp_->getInstrument().setMetaValue(<span class="stringliteral">"#comment"</span>, <a class="code" href="classOpenMS_1_1String.html">String</a>(transcoded_chars));</div>
<div class="line"><a name="l00864"></a><span class="lineno"> 864</span>  }</div>
<div class="line"><a name="l00865"></a><span class="lineno"> 865</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"dataProcessing"</span>)</div>
<div class="line"><a name="l00866"></a><span class="lineno"> 866</span>  {</div>
<div class="line"><a name="l00867"></a><span class="lineno"> 867</span>  <span class="comment">//this is currently ignored</span></div>
<div class="line"><a name="l00868"></a><span class="lineno"> 868</span>  }</div>
<div class="line"><a name="l00869"></a><span class="lineno"> 869</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (parent_tag == <span class="stringliteral">"scan"</span>)</div>
<div class="line"><a name="l00870"></a><span class="lineno"> 870</span>  {</div>
<div class="line"><a name="l00871"></a><span class="lineno"> 871</span>  exp_->getSpectra().back().setComment(transcoded_chars);</div>
<div class="line"><a name="l00872"></a><span class="lineno"> 872</span>  }</div>
<div class="line"><a name="l00873"></a><span class="lineno"> 873</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1String.html">String</a>(transcoded_chars).trim() != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00874"></a><span class="lineno"> 874</span>  {</div>
<div class="line"><a name="l00875"></a><span class="lineno"> 875</span>  warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Unhandled comment '"</span>) + transcoded_chars + <span class="stringliteral">"' in element '"</span> + open_tags_.back() + <span class="stringliteral">"'"</span>);</div>
<div class="line"><a name="l00876"></a><span class="lineno"> 876</span>  }</div>
<div class="line"><a name="l00877"></a><span class="lineno"> 877</span>  }</div>
<div class="line"><a name="l00878"></a><span class="lineno"> 878</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1String.html">String</a>(transcoded_chars).<a class="code" href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">trim</a>() != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00879"></a><span class="lineno"> 879</span>  {</div>
<div class="line"><a name="l00880"></a><span class="lineno"> 880</span>  warning(LOAD, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Unhandled character content '"</span>) + transcoded_chars + <span class="stringliteral">"' in element '"</span> + open_tags_.back() + <span class="stringliteral">"'"</span>);</div>
<div class="line"><a name="l00881"></a><span class="lineno"> 881</span>  }</div>
<div class="line"><a name="l00882"></a><span class="lineno"> 882</span>  }</div>
<div class="line"><a name="l00883"></a><span class="lineno"> 883</span> </div>
<div class="line"><a name="l00884"></a><span class="lineno"> 884</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> MapType></div>
<div class="line"><a name="l00885"></a><span class="lineno"><a class="line" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a0038ff865ac073e00ca829d977f2ccdf"> 885</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a0038ff865ac073e00ca829d977f2ccdf">MzXMLHandler<MapType>::writeTo</a>(std::ostream& os)</div>
<div class="line"><a name="l00886"></a><span class="lineno"> 886</span>  {</div>
<div class="line"><a name="l00887"></a><span class="lineno"> 887</span>  <span class="comment">//determine how many spectra there are (count only those with peaks)</span></div>
<div class="line"><a name="l00888"></a><span class="lineno"> 888</span>  <a class="code" href="classunsigned_01int.html">UInt</a> count_tmp_ = 0;</div>
<div class="line"><a name="l00889"></a><span class="lineno"> 889</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s < cexp_->size(); s++)</div>
<div class="line"><a name="l00890"></a><span class="lineno"> 890</span>  {</div>
<div class="line"><a name="l00891"></a><span class="lineno"> 891</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>& spec = (*cexp_)[s];</div>
<div class="line"><a name="l00892"></a><span class="lineno"> 892</span>  <span class="keywordflow">if</span> (spec.size() != 0)</div>
<div class="line"><a name="l00893"></a><span class="lineno"> 893</span>  ++count_tmp_;</div>
<div class="line"><a name="l00894"></a><span class="lineno"> 894</span>  }</div>
<div class="line"><a name="l00895"></a><span class="lineno"> 895</span>  <span class="keywordflow">if</span> (count_tmp_ == 0)</div>
<div class="line"><a name="l00896"></a><span class="lineno"> 896</span>  ++count_tmp_;</div>
<div class="line"><a name="l00897"></a><span class="lineno"> 897</span>  logger_.startProgress(0, cexp_->size(), <span class="stringliteral">"storing mzXML file"</span>);</div>
<div class="line"><a name="l00898"></a><span class="lineno"> 898</span>  os << <span class="stringliteral">"<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n"</span></div>
<div class="line"><a name="l00899"></a><span class="lineno"> 899</span>  << <span class="stringliteral">"<mzXML xmlns=\"http://sashimi.sourceforge.net/schema_revision/mzXML_2.1\" "</span></div>
<div class="line"><a name="l00900"></a><span class="lineno"> 900</span>  << <span class="stringliteral">"xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" "</span></div>
<div class="line"><a name="l00901"></a><span class="lineno"> 901</span>  << <span class="stringliteral">"xsi:schemaLocation=\"http://sashimi.sourceforge.net/schema_revision/mzXML_2.1 "</span></div>
<div class="line"><a name="l00902"></a><span class="lineno"> 902</span>  << <span class="stringliteral">"http://sashimi.sourceforge.net/schema_revision/mzXML_2.1/mzXML_idx_2.1.xsd\">\n"</span></div>
<div class="line"><a name="l00903"></a><span class="lineno"> 903</span>  << <span class="stringliteral">"\t<msRun scanCount=\""</span> << count_tmp_ << <span class="stringliteral">"\">\n"</span>;</div>
<div class="line"><a name="l00904"></a><span class="lineno"> 904</span> </div>
<div class="line"><a name="l00905"></a><span class="lineno"> 905</span>  <span class="comment">//----------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00906"></a><span class="lineno"> 906</span>  <span class="comment">// parent files</span></div>
<div class="line"><a name="l00907"></a><span class="lineno"> 907</span>  <span class="comment">//----------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00908"></a><span class="lineno"> 908</span>  <span class="keywordflow">if</span> (cexp_->getSourceFiles().empty())</div>
<div class="line"><a name="l00909"></a><span class="lineno"> 909</span>  {</div>
<div class="line"><a name="l00910"></a><span class="lineno"> 910</span>  os << <span class="stringliteral">"\t\t<parentFile fileName=\"\" fileType=\"processedData\" fileSha1=\"0000000000000000000000000000000000000000\"/>\n"</span>;</div>
<div class="line"><a name="l00911"></a><span class="lineno"> 911</span>  }</div>
<div class="line"><a name="l00912"></a><span class="lineno"> 912</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00913"></a><span class="lineno"> 913</span>  {</div>
<div class="line"><a name="l00914"></a><span class="lineno"> 914</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < cexp_->getSourceFiles().size(); ++i)</div>
<div class="line"><a name="l00915"></a><span class="lineno"> 915</span>  {</div>
<div class="line"><a name="l00916"></a><span class="lineno"> 916</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SourceFile.html">SourceFile</a>& sf = cexp_->getSourceFiles()[i];</div>
<div class="line"><a name="l00917"></a><span class="lineno"> 917</span>  os << <span class="stringliteral">"\t\t<parentFile fileName=\""</span> << sf.<a class="code" href="classOpenMS_1_1SourceFile.html#acadddeff186604f0185315e70aab94fb">getNameOfFile</a>() << <span class="stringliteral">"\" fileType=\""</span>;</div>
<div class="line"><a name="l00918"></a><span class="lineno"> 918</span>  <span class="comment">//file type is an enum in mzXML => search for 'raw' string</span></div>
<div class="line"><a name="l00919"></a><span class="lineno"> 919</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> tmp_string = sf.<a class="code" href="classOpenMS_1_1SourceFile.html#ac82b3cc3ba4c24b0ab9768fede8c3c9c">getFileType</a>();</div>
<div class="line"><a name="l00920"></a><span class="lineno"> 920</span>  tmp_string.<a class="code" href="classOpenMS_1_1String.html#a8fd5f3c864af3d60885cc09888dd18d3">toLower</a>();</div>
<div class="line"><a name="l00921"></a><span class="lineno"> 921</span>  <span class="keywordflow">if</span> (tmp_string.<a class="code" href="classOpenMS_1_1String.html#ad0f3113f29d5d2ebdfa090bab2cef7ac">hasSubstring</a>(<span class="stringliteral">"raw"</span>))</div>
<div class="line"><a name="l00922"></a><span class="lineno"> 922</span>  {</div>
<div class="line"><a name="l00923"></a><span class="lineno"> 923</span>  os << <span class="stringliteral">"RAWData"</span>;</div>
<div class="line"><a name="l00924"></a><span class="lineno"> 924</span>  }</div>
<div class="line"><a name="l00925"></a><span class="lineno"> 925</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00926"></a><span class="lineno"> 926</span>  {</div>
<div class="line"><a name="l00927"></a><span class="lineno"> 927</span>  os << <span class="stringliteral">"processedData"</span>;</div>
<div class="line"><a name="l00928"></a><span class="lineno"> 928</span>  }</div>
<div class="line"><a name="l00929"></a><span class="lineno"> 929</span>  <span class="comment">//Sha1 checksum must have 40 characters => create a fake if it is unknown</span></div>
<div class="line"><a name="l00930"></a><span class="lineno"> 930</span>  os << <span class="stringliteral">"\" fileSha1=\""</span>;</div>
<div class="line"><a name="l00931"></a><span class="lineno"> 931</span>  tmp_string = sf.<a class="code" href="classOpenMS_1_1SourceFile.html#a5469cd06bde314b8524d14cd76df2cd1">getChecksum</a>();</div>
<div class="line"><a name="l00932"></a><span class="lineno"> 932</span>  <span class="keywordflow">if</span> (sf.<a class="code" href="classOpenMS_1_1SourceFile.html#a5469cd06bde314b8524d14cd76df2cd1">getChecksum</a>().size() != 40 || sf.<a class="code" href="classOpenMS_1_1SourceFile.html#a2bf1ca8186169631f23edd67ddbd45e1">getChecksumType</a>() != <a class="code" href="classOpenMS_1_1SourceFile.html#a6440df7f4dbfc4c3370e2b6781bc74e5a27028cc8b5d6f0a1cb3030c180019abc">SourceFile::SHA1</a>)</div>
<div class="line"><a name="l00933"></a><span class="lineno"> 933</span>  {</div>
<div class="line"><a name="l00934"></a><span class="lineno"> 934</span>  os << <span class="stringliteral">"0000000000000000000000000000000000000000"</span>;</div>
<div class="line"><a name="l00935"></a><span class="lineno"> 935</span>  }</div>
<div class="line"><a name="l00936"></a><span class="lineno"> 936</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00937"></a><span class="lineno"> 937</span>  {</div>
<div class="line"><a name="l00938"></a><span class="lineno"> 938</span>  os << sf.<a class="code" href="classOpenMS_1_1SourceFile.html#a5469cd06bde314b8524d14cd76df2cd1">getChecksum</a>();</div>
<div class="line"><a name="l00939"></a><span class="lineno"> 939</span>  }</div>
<div class="line"><a name="l00940"></a><span class="lineno"> 940</span>  os << <span class="stringliteral">"\"/>\n"</span>;</div>
<div class="line"><a name="l00941"></a><span class="lineno"> 941</span>  }</div>
<div class="line"><a name="l00942"></a><span class="lineno"> 942</span>  }</div>
<div class="line"><a name="l00943"></a><span class="lineno"> 943</span> </div>
<div class="line"><a name="l00944"></a><span class="lineno"> 944</span>  <span class="comment">//----------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00945"></a><span class="lineno"> 945</span>  <span class="comment">//instrument</span></div>
<div class="line"><a name="l00946"></a><span class="lineno"> 946</span>  <span class="comment">//----------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00947"></a><span class="lineno"> 947</span>  <span class="keywordflow">if</span> (cexp_->getInstrument() != <a class="code" href="classOpenMS_1_1Instrument.html">Instrument</a>() || cexp_->getContacts().size() != 0)</div>
<div class="line"><a name="l00948"></a><span class="lineno"> 948</span>  {</div>
<div class="line"><a name="l00949"></a><span class="lineno"> 949</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Instrument.html">Instrument</a>& inst = cexp_->getInstrument();</div>
<div class="line"><a name="l00950"></a><span class="lineno"> 950</span>  os << <span class="stringliteral">"\t\t<msInstrument>\n"</span></div>
<div class="line"><a name="l00951"></a><span class="lineno"> 951</span>  << <span class="stringliteral">"\t\t\t<msManufacturer category=\"msManufacturer\" value=\""</span> << inst.<a class="code" href="classOpenMS_1_1Instrument.html#adeb3a96bea31dcca5dc2cba4d6e22cb5">getVendor</a>() << <span class="stringliteral">"\"/>\n"</span> << <span class="stringliteral">"\t\t\t<msModel category=\"msModel\" value=\""</span> << inst.<a class="code" href="classOpenMS_1_1Instrument.html#a307ba40c92040f24cb0b496fb5b58b88">getModel</a>() << <span class="stringliteral">"\"/>\n"</span>;</div>
<div class="line"><a name="l00952"></a><span class="lineno"> 952</span>  <span class="keywordflow">if</span> (inst.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>().empty() || !inst.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>()[0].getIonizationMethod())</div>
<div class="line"><a name="l00953"></a><span class="lineno"> 953</span>  {</div>
<div class="line"><a name="l00954"></a><span class="lineno"> 954</span>  os << <span class="stringliteral">"\t\t\t<msIonisation category=\"msIonisation\" value=\"\"/>\n"</span>;</div>
<div class="line"><a name="l00955"></a><span class="lineno"> 955</span>  }</div>
<div class="line"><a name="l00956"></a><span class="lineno"> 956</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00957"></a><span class="lineno"> 957</span>  {</div>
<div class="line"><a name="l00958"></a><span class="lineno"> 958</span>  os << <span class="stringliteral">"\t\t\t<msIonisation category=\"msIonisation\" value=\""</span> << cv_terms_[2][inst.<a class="code" href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">getIonSources</a>()[0].getIonizationMethod()] << <span class="stringliteral">"\"/>\n"</span>;</div>
<div class="line"><a name="l00959"></a><span class="lineno"> 959</span>  }</div>
<div class="line"><a name="l00960"></a><span class="lineno"> 960</span>  <span class="keyword">const</span> std::vector<MassAnalyzer>& analyzers = inst.<a class="code" href="classOpenMS_1_1Instrument.html#af3feca15695c5ad09a91b35d43559e57">getMassAnalyzers</a>();</div>
<div class="line"><a name="l00961"></a><span class="lineno"> 961</span>  <span class="keywordflow">if</span> (analyzers.empty() || !analyzers[0].getResolutionMethod())</div>
<div class="line"><a name="l00962"></a><span class="lineno"> 962</span>  {</div>
<div class="line"><a name="l00963"></a><span class="lineno"> 963</span>  os << <span class="stringliteral">"\t\t\t<msMassAnalyzer category=\"msMassAnalyzer\" value=\"\"/>\n"</span>;</div>
<div class="line"><a name="l00964"></a><span class="lineno"> 964</span>  }</div>
<div class="line"><a name="l00965"></a><span class="lineno"> 965</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00966"></a><span class="lineno"> 966</span>  {</div>
<div class="line"><a name="l00967"></a><span class="lineno"> 967</span>  os << <span class="stringliteral">"\t\t\t<msMassAnalyzer category=\"msMassAnalyzer\" value=\""</span> << cv_terms_[3][analyzers[0].getType()] << <span class="stringliteral">"\"/>\n"</span>;</div>
<div class="line"><a name="l00968"></a><span class="lineno"> 968</span>  }</div>
<div class="line"><a name="l00969"></a><span class="lineno"> 969</span>  <span class="keywordflow">if</span> (inst.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>().empty() || !inst.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>()[0].getType())</div>
<div class="line"><a name="l00970"></a><span class="lineno"> 970</span>  {</div>
<div class="line"><a name="l00971"></a><span class="lineno"> 971</span>  os << <span class="stringliteral">"\t\t\t<msDetector category=\"msDetector\" value=\"\"/>\n"</span>;</div>
<div class="line"><a name="l00972"></a><span class="lineno"> 972</span>  }</div>
<div class="line"><a name="l00973"></a><span class="lineno"> 973</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00974"></a><span class="lineno"> 974</span>  {</div>
<div class="line"><a name="l00975"></a><span class="lineno"> 975</span>  os << <span class="stringliteral">"\t\t\t<msDetector category=\"msDetector\" value=\""</span> << cv_terms_[4][inst.<a class="code" href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">getIonDetectors</a>()[0].getType()] << <span class="stringliteral">"\"/>\n"</span>;</div>
<div class="line"><a name="l00976"></a><span class="lineno"> 976</span>  }</div>
<div class="line"><a name="l00977"></a><span class="lineno"> 977</span>  os << <span class="stringliteral">"\t\t\t<software type=\"acquisition\" name=\""</span> << inst.<a class="code" href="classOpenMS_1_1Instrument.html#a219795d06917877c7d946a00f23e2319">getSoftware</a>().<a class="code" href="classOpenMS_1_1Software.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>() << <span class="stringliteral">"\" version=\""</span> << inst.<a class="code" href="classOpenMS_1_1Instrument.html#a219795d06917877c7d946a00f23e2319">getSoftware</a>().<a class="code" href="classOpenMS_1_1Software.html#ae6b3b4b6857bc1987282e2f29611dd41">getVersion</a>() << <span class="stringliteral">"\"/>\n"</span>;</div>
<div class="line"><a name="l00978"></a><span class="lineno"> 978</span>  <span class="keywordflow">if</span> (analyzers.empty() || !analyzers[0].getResolutionMethod())</div>
<div class="line"><a name="l00979"></a><span class="lineno"> 979</span>  {</div>
<div class="line"><a name="l00980"></a><span class="lineno"> 980</span>  os << <span class="stringliteral">"\t\t\t<msResolution category=\"msResolution\" value=\"\"/>\n"</span>;</div>
<div class="line"><a name="l00981"></a><span class="lineno"> 981</span>  }</div>
<div class="line"><a name="l00982"></a><span class="lineno"> 982</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00983"></a><span class="lineno"> 983</span>  {</div>
<div class="line"><a name="l00984"></a><span class="lineno"> 984</span>  os << <span class="stringliteral">"\t\t\t<msResolution category=\"msResolution\" value=\""</span> << cv_terms_[5][analyzers[0].getResolutionMethod()] << <span class="stringliteral">"\"/>\n"</span>;</div>
<div class="line"><a name="l00985"></a><span class="lineno"> 985</span>  }</div>
<div class="line"><a name="l00986"></a><span class="lineno"> 986</span> </div>
<div class="line"><a name="l00987"></a><span class="lineno"> 987</span>  <span class="keywordflow">if</span> (cexp_->getContacts().size() > 0)</div>
<div class="line"><a name="l00988"></a><span class="lineno"> 988</span>  {</div>
<div class="line"><a name="l00989"></a><span class="lineno"> 989</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1ContactPerson.html">ContactPerson</a>& cont = cexp_->getContacts()[0];</div>
<div class="line"><a name="l00990"></a><span class="lineno"> 990</span> </div>
<div class="line"><a name="l00991"></a><span class="lineno"> 991</span>  os << <span class="stringliteral">"\t\t\t<operator first=\""</span> << cont.<a class="code" href="classOpenMS_1_1ContactPerson.html#ac02fa25060dabd021d726903e7d0d2ea">getFirstName</a>() << <span class="stringliteral">"\" last=\""</span> << cont.<a class="code" href="classOpenMS_1_1ContactPerson.html#a36df0ae8f5b0e98a1e0009ccbf8e1972">getLastName</a>() << <span class="stringliteral">"\""</span>;</div>
<div class="line"><a name="l00992"></a><span class="lineno"> 992</span> </div>
<div class="line"><a name="l00993"></a><span class="lineno"> 993</span>  <span class="keywordflow">if</span> (cont.<a class="code" href="classOpenMS_1_1ContactPerson.html#aa40d949517afa236a88a9eb41ea4f35c">getEmail</a>() != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00994"></a><span class="lineno"> 994</span>  {</div>
<div class="line"><a name="l00995"></a><span class="lineno"> 995</span>  os << <span class="stringliteral">" email=\""</span> << cont.<a class="code" href="classOpenMS_1_1ContactPerson.html#aa40d949517afa236a88a9eb41ea4f35c">getEmail</a>() << <span class="stringliteral">"\""</span>;</div>
<div class="line"><a name="l00996"></a><span class="lineno"> 996</span>  }</div>
<div class="line"><a name="l00997"></a><span class="lineno"> 997</span> </div>
<div class="line"><a name="l00998"></a><span class="lineno"> 998</span>  <span class="keywordflow">if</span> (cont.<a class="code" href="classOpenMS_1_1ContactPerson.html#a9d7de80efbcfc8f49025772de7806a23">getURL</a>() != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00999"></a><span class="lineno"> 999</span>  {</div>
<div class="line"><a name="l01000"></a><span class="lineno"> 1000</span>  os << <span class="stringliteral">" URI=\""</span> << cont.<a class="code" href="classOpenMS_1_1ContactPerson.html#a9d7de80efbcfc8f49025772de7806a23">getURL</a>() << <span class="stringliteral">"\""</span>;</div>
<div class="line"><a name="l01001"></a><span class="lineno"> 1001</span>  }</div>
<div class="line"><a name="l01002"></a><span class="lineno"> 1002</span> </div>
<div class="line"><a name="l01003"></a><span class="lineno"> 1003</span>  <span class="keywordflow">if</span> (cont.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#acabf8a0e3c40224df62b282a5ce0318f">metaValueExists</a>(<span class="stringliteral">"#phone"</span>))</div>
<div class="line"><a name="l01004"></a><span class="lineno"> 1004</span>  {</div>
<div class="line"><a name="l01005"></a><span class="lineno"> 1005</span>  os << <span class="stringliteral">" phone=\""</span> << (<a class="code" href="classOpenMS_1_1String.html">String</a>)(cont.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(<span class="stringliteral">"#phone"</span>)) << <span class="stringliteral">"\""</span>;</div>
<div class="line"><a name="l01006"></a><span class="lineno"> 1006</span>  }</div>
<div class="line"><a name="l01007"></a><span class="lineno"> 1007</span> </div>
<div class="line"><a name="l01008"></a><span class="lineno"> 1008</span>  os << <span class="stringliteral">"/>\n"</span>;</div>
<div class="line"><a name="l01009"></a><span class="lineno"> 1009</span>  }</div>
<div class="line"><a name="l01010"></a><span class="lineno"> 1010</span>  writeUserParam_(os, inst, 3);</div>
<div class="line"><a name="l01011"></a><span class="lineno"> 1011</span> </div>
<div class="line"><a name="l01012"></a><span class="lineno"> 1012</span>  <span class="keywordflow">if</span> (inst.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#acabf8a0e3c40224df62b282a5ce0318f">metaValueExists</a>(<span class="stringliteral">"#comment"</span>))</div>
<div class="line"><a name="l01013"></a><span class="lineno"> 1013</span>  {</div>
<div class="line"><a name="l01014"></a><span class="lineno"> 1014</span>  os << <span class="stringliteral">"\t\t\t<comment>"</span> << inst.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(<span class="stringliteral">"#comment"</span>) << <span class="stringliteral">"</comment>\n"</span>;</div>
<div class="line"><a name="l01015"></a><span class="lineno"> 1015</span>  }</div>
<div class="line"><a name="l01016"></a><span class="lineno"> 1016</span> </div>
<div class="line"><a name="l01017"></a><span class="lineno"> 1017</span>  os << <span class="stringliteral">"\t\t</msInstrument>\n"</span>;</div>
<div class="line"><a name="l01018"></a><span class="lineno"> 1018</span>  }</div>
<div class="line"><a name="l01019"></a><span class="lineno"> 1019</span> </div>
<div class="line"><a name="l01020"></a><span class="lineno"> 1020</span>  <span class="comment">//----------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l01021"></a><span class="lineno"> 1021</span>  <span class="comment">//data processing (the information of the first spectrum is assigned to the whole file)</span></div>
<div class="line"><a name="l01022"></a><span class="lineno"> 1022</span>  <span class="comment">//----------------------------------------------------------------------------------------</span></div>
<div class="line"><a name="l01023"></a><span class="lineno"> 1023</span>  <span class="keywordflow">if</span> (cexp_->size() == 0 || (*cexp_)[0].getDataProcessing().empty())</div>
<div class="line"><a name="l01024"></a><span class="lineno"> 1024</span>  {</div>
<div class="line"><a name="l01025"></a><span class="lineno"> 1025</span>  os << <span class="stringliteral">"\t\t<dataProcessing>\n"</span></div>
<div class="line"><a name="l01026"></a><span class="lineno"> 1026</span>  << <span class="stringliteral">"\t\t\t<software type=\"processing\" name=\"\" version=\"\"/>\n"</span></div>
<div class="line"><a name="l01027"></a><span class="lineno"> 1027</span>  << <span class="stringliteral">"\t\t</dataProcessing>\n"</span>;</div>
<div class="line"><a name="l01028"></a><span class="lineno"> 1028</span>  }</div>
<div class="line"><a name="l01029"></a><span class="lineno"> 1029</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01030"></a><span class="lineno"> 1030</span>  {</div>
<div class="line"><a name="l01031"></a><span class="lineno"> 1031</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < (*cexp_)[0].getDataProcessing().size(); ++i)</div>
<div class="line"><a name="l01032"></a><span class="lineno"> 1032</span>  {</div>
<div class="line"><a name="l01033"></a><span class="lineno"> 1033</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1DataProcessing.html">DataProcessing</a>& data_processing = (*cexp_)[0].getDataProcessing()[i];</div>
<div class="line"><a name="l01034"></a><span class="lineno"> 1034</span>  os << <span class="stringliteral">"\t\t<dataProcessing deisotoped=\""</span></div>
<div class="line"><a name="l01035"></a><span class="lineno"> 1035</span>  << data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#ad34bb2f8f677e2f6c6c505d11754a765">getProcessingActions</a>().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a1491834ae41afad2cd5d4e69f20aaaae">DataProcessing::DEISOTOPING</a>)</div>
<div class="line"><a name="l01036"></a><span class="lineno"> 1036</span>  << <span class="stringliteral">"\" chargeDeconvoluted=\""</span></div>
<div class="line"><a name="l01037"></a><span class="lineno"> 1037</span>  << data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#ad34bb2f8f677e2f6c6c505d11754a765">getProcessingActions</a>().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ad6aaf5187119b5738f4648dcb932c240">DataProcessing::CHARGE_DECONVOLUTION</a>)</div>
<div class="line"><a name="l01038"></a><span class="lineno"> 1038</span>  << <span class="stringliteral">"\" centroided=\""</span></div>
<div class="line"><a name="l01039"></a><span class="lineno"> 1039</span>  << data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#ad34bb2f8f677e2f6c6c505d11754a765">getProcessingActions</a>().count(<a class="code" href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a181a4b8e81bcfae30e38dc548a5586f3">DataProcessing::PEAK_PICKING</a>)</div>
<div class="line"><a name="l01040"></a><span class="lineno"> 1040</span>  << <span class="stringliteral">"\""</span>;</div>
<div class="line"><a name="l01041"></a><span class="lineno"> 1041</span>  <span class="keywordflow">if</span> (data_processing.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#acabf8a0e3c40224df62b282a5ce0318f">metaValueExists</a>(<span class="stringliteral">"#intensity_cutoff"</span>))</div>
<div class="line"><a name="l01042"></a><span class="lineno"> 1042</span>  {</div>
<div class="line"><a name="l01043"></a><span class="lineno"> 1043</span>  os << <span class="stringliteral">" intensityCutoff=\""</span> << data_processing.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(<span class="stringliteral">"#intensity_cutoff"</span>).<a class="code" href="classOpenMS_1_1DataValue.html#a82e960f65e28ae6aba1271adbb83236e">toString</a>() << <span class="stringliteral">"\""</span>;</div>
<div class="line"><a name="l01044"></a><span class="lineno"> 1044</span>  }</div>
<div class="line"><a name="l01045"></a><span class="lineno"> 1045</span>  os << <span class="stringliteral">">\n"</span></div>
<div class="line"><a name="l01046"></a><span class="lineno"> 1046</span>  << <span class="stringliteral">"\t\t\t<software type=\""</span>;</div>
<div class="line"><a name="l01047"></a><span class="lineno"> 1047</span>  <span class="keywordflow">if</span> (data_processing.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#acabf8a0e3c40224df62b282a5ce0318f">metaValueExists</a>(<span class="stringliteral">"#type"</span>))</div>
<div class="line"><a name="l01048"></a><span class="lineno"> 1048</span>  {</div>
<div class="line"><a name="l01049"></a><span class="lineno"> 1049</span>  os << data_processing.<a class="code" href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">getMetaValue</a>(<span class="stringliteral">"#type"</span>).<a class="code" href="classOpenMS_1_1DataValue.html#a82e960f65e28ae6aba1271adbb83236e">toString</a>();</div>
<div class="line"><a name="l01050"></a><span class="lineno"> 1050</span>  }</div>
<div class="line"><a name="l01051"></a><span class="lineno"> 1051</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01052"></a><span class="lineno"> 1052</span>  {</div>
<div class="line"><a name="l01053"></a><span class="lineno"> 1053</span>  os << <span class="stringliteral">"processing"</span>;</div>
<div class="line"><a name="l01054"></a><span class="lineno"> 1054</span>  }</div>
<div class="line"><a name="l01055"></a><span class="lineno"> 1055</span> </div>
<div class="line"><a name="l01056"></a><span class="lineno"> 1056</span>  os << <span class="stringliteral">"\" name=\""</span> << data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#a219795d06917877c7d946a00f23e2319">getSoftware</a>().<a class="code" href="classOpenMS_1_1Software.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a>()</div>
<div class="line"><a name="l01057"></a><span class="lineno"> 1057</span>  << <span class="stringliteral">"\" version=\""</span> << data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#a219795d06917877c7d946a00f23e2319">getSoftware</a>().<a class="code" href="classOpenMS_1_1Software.html#ae6b3b4b6857bc1987282e2f29611dd41">getVersion</a>();</div>
<div class="line"><a name="l01058"></a><span class="lineno"> 1058</span> </div>
<div class="line"><a name="l01059"></a><span class="lineno"> 1059</span>  <span class="keywordflow">if</span> (data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#a3bbd5b209e18f9afd4d8b4308787a538">getCompletionTime</a>() != <a class="code" href="classOpenMS_1_1DateTime.html">DateTime</a>())</div>
<div class="line"><a name="l01060"></a><span class="lineno"> 1060</span>  {</div>
<div class="line"><a name="l01061"></a><span class="lineno"> 1061</span>  os << <span class="stringliteral">"\" completionTime=\""</span> << data_processing.<a class="code" href="classOpenMS_1_1DataProcessing.html#a3bbd5b209e18f9afd4d8b4308787a538">getCompletionTime</a>().<a class="code" href="classOpenMS_1_1DateTime.html#ae8d3cac5cd5763984d9ca84d3453ed28">get</a>().substitute(<span class="charliteral">' '</span>, <span class="charliteral">'T'</span>);</div>
<div class="line"><a name="l01062"></a><span class="lineno"> 1062</span>  }</div>
<div class="line"><a name="l01063"></a><span class="lineno"> 1063</span>  os << <span class="stringliteral">"\"/>\n"</span>;</div>
<div class="line"><a name="l01064"></a><span class="lineno"> 1064</span>  writeUserParam_(os, data_processing, 3, <span class="stringliteral">"processingOperation"</span>);</div>
<div class="line"><a name="l01065"></a><span class="lineno"> 1065</span> </div>
<div class="line"><a name="l01066"></a><span class="lineno"> 1066</span>  os << <span class="stringliteral">"\t\t</dataProcessing>\n"</span>;</div>
<div class="line"><a name="l01067"></a><span class="lineno"> 1067</span>  }</div>
<div class="line"><a name="l01068"></a><span class="lineno"> 1068</span>  }</div>
<div class="line"><a name="l01069"></a><span class="lineno"> 1069</span> </div>
<div class="line"><a name="l01070"></a><span class="lineno"> 1070</span>  <span class="comment">//check if the nativeID of all spectra are numbers or numbers prefixed with 'scan='</span></div>
<div class="line"><a name="l01071"></a><span class="lineno"> 1071</span>  <span class="comment">//If not we need to renumber all spectra.</span></div>
<div class="line"><a name="l01072"></a><span class="lineno"> 1072</span>  <span class="keywordtype">bool</span> all_numbers = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01073"></a><span class="lineno"> 1073</span>  <span class="keywordtype">bool</span> all_empty = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01074"></a><span class="lineno"> 1074</span>  <span class="keywordtype">bool</span> all_prefixed_numbers = <span class="keyword">true</span>;</div>
<div class="line"><a name="l01075"></a><span class="lineno"> 1075</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s < cexp_->size(); s++)</div>
<div class="line"><a name="l01076"></a><span class="lineno"> 1076</span>  {</div>
<div class="line"><a name="l01077"></a><span class="lineno"> 1077</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> native_id = (*cexp_)[s].getNativeID();</div>
<div class="line"><a name="l01078"></a><span class="lineno"> 1078</span>  <span class="keywordflow">if</span> (!native_id.<a class="code" href="classOpenMS_1_1String.html#ae1870a969417d19a33f225046a66a58d">hasPrefix</a>(<span class="stringliteral">"scan="</span>))</div>
<div class="line"><a name="l01079"></a><span class="lineno"> 1079</span>  {</div>
<div class="line"><a name="l01080"></a><span class="lineno"> 1080</span>  all_prefixed_numbers = <span class="keyword">false</span>;</div>
<div class="line"><a name="l01081"></a><span class="lineno"> 1081</span>  }</div>
<div class="line"><a name="l01082"></a><span class="lineno"> 1082</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01083"></a><span class="lineno"> 1083</span>  {</div>
<div class="line"><a name="l01084"></a><span class="lineno"> 1084</span>  native_id = native_id.<a class="code" href="classOpenMS_1_1String.html#a226b41d565aa586bd45aa7d046608511">substr</a>(5);</div>
<div class="line"><a name="l01085"></a><span class="lineno"> 1085</span>  }</div>
<div class="line"><a name="l01086"></a><span class="lineno"> 1086</span>  <span class="keywordflow">try</span></div>
<div class="line"><a name="l01087"></a><span class="lineno"> 1087</span>  {</div>
<div class="line"><a name="l01088"></a><span class="lineno"> 1088</span>  native_id.<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>();</div>
<div class="line"><a name="l01089"></a><span class="lineno"> 1089</span>  }</div>
<div class="line"><a name="l01090"></a><span class="lineno"> 1090</span>  <span class="keywordflow">catch</span> (<a class="code" href="classOpenMS_1_1Exception_1_1ConversionError.html">Exception::ConversionError</a>&)</div>
<div class="line"><a name="l01091"></a><span class="lineno"> 1091</span>  {</div>
<div class="line"><a name="l01092"></a><span class="lineno"> 1092</span>  all_numbers = <span class="keyword">false</span>;</div>
<div class="line"><a name="l01093"></a><span class="lineno"> 1093</span>  all_prefixed_numbers = <span class="keyword">false</span>;</div>
<div class="line"><a name="l01094"></a><span class="lineno"> 1094</span>  <span class="keywordflow">if</span> (native_id != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l01095"></a><span class="lineno"> 1095</span>  {</div>
<div class="line"><a name="l01096"></a><span class="lineno"> 1096</span>  all_empty = <span class="keyword">false</span>;</div>
<div class="line"><a name="l01097"></a><span class="lineno"> 1097</span>  }</div>
<div class="line"><a name="l01098"></a><span class="lineno"> 1098</span>  }</div>
<div class="line"><a name="l01099"></a><span class="lineno"> 1099</span>  }</div>
<div class="line"><a name="l01100"></a><span class="lineno"> 1100</span>  <span class="comment">//If we need to renumber and the nativeIDs were not empty, warn the user</span></div>
<div class="line"><a name="l01101"></a><span class="lineno"> 1101</span>  <span class="keywordflow">if</span> (!all_numbers && !all_empty)</div>
<div class="line"><a name="l01102"></a><span class="lineno"> 1102</span>  {</div>
<div class="line"><a name="l01103"></a><span class="lineno"> 1103</span>  warning(STORE, <span class="stringliteral">"Not all spectrum native IDs are numbers or correctly prefixed with 'scan='. The spectra are renumbered and the native IDs are lost!"</span>);</div>
<div class="line"><a name="l01104"></a><span class="lineno"> 1104</span>  }</div>
<div class="line"><a name="l01105"></a><span class="lineno"> 1105</span> </div>
<div class="line"><a name="l01106"></a><span class="lineno"> 1106</span>  <span class="comment">// write scans</span></div>
<div class="line"><a name="l01107"></a><span class="lineno"> 1107</span>  std::stack<UInt> open_scans;</div>
<div class="line"><a name="l01108"></a><span class="lineno"> 1108</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> s = 0; s < cexp_->size(); s++)</div>
<div class="line"><a name="l01109"></a><span class="lineno"> 1109</span>  {</div>
<div class="line"><a name="l01110"></a><span class="lineno"> 1110</span>  logger_.setProgress(s);</div>
<div class="line"><a name="l01111"></a><span class="lineno"> 1111</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">SpectrumType</a>& spec = (*cexp_)[s];</div>
<div class="line"><a name="l01112"></a><span class="lineno"> 1112</span> </div>
<div class="line"><a name="l01113"></a><span class="lineno"> 1113</span>  <a class="code" href="classunsigned_01int.html">UInt</a> ms_level = spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a1726d12d7597baa9fca0c1da0492f3da">getMSLevel</a>();</div>
<div class="line"><a name="l01114"></a><span class="lineno"> 1114</span>  open_scans.push(ms_level);</div>
<div class="line"><a name="l01115"></a><span class="lineno"> 1115</span> </div>
<div class="line"><a name="l01116"></a><span class="lineno"> 1116</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> spectrum_id = s + 1;</div>
<div class="line"><a name="l01117"></a><span class="lineno"> 1117</span>  <span class="keywordflow">if</span> (all_prefixed_numbers)</div>
<div class="line"><a name="l01118"></a><span class="lineno"> 1118</span>  {</div>
<div class="line"><a name="l01119"></a><span class="lineno"> 1119</span>  spectrum_id = spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ad368341c22d3447e324134c47adff081">getNativeID</a>().<a class="code" href="classOpenMS_1_1String.html#a226b41d565aa586bd45aa7d046608511">substr</a>(5).<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>();</div>
<div class="line"><a name="l01120"></a><span class="lineno"> 1120</span>  }</div>
<div class="line"><a name="l01121"></a><span class="lineno"> 1121</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (all_numbers)</div>
<div class="line"><a name="l01122"></a><span class="lineno"> 1122</span>  {</div>
<div class="line"><a name="l01123"></a><span class="lineno"> 1123</span>  spectrum_id = spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#ad368341c22d3447e324134c47adff081">getNativeID</a>().<a class="code" href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">toInt</a>();</div>
<div class="line"><a name="l01124"></a><span class="lineno"> 1124</span>  }</div>
<div class="line"><a name="l01125"></a><span class="lineno"> 1125</span> </div>
<div class="line"><a name="l01126"></a><span class="lineno"> 1126</span>  os << <a class="code" href="classOpenMS_1_1String.html">String</a>(ms_level + 1, <span class="charliteral">'\t'</span>)</div>
<div class="line"><a name="l01127"></a><span class="lineno"> 1127</span>  << <span class="stringliteral">"<scan num=\""</span> << spectrum_id << <span class="stringliteral">"\" msLevel=\""</span></div>
<div class="line"><a name="l01128"></a><span class="lineno"> 1128</span>  << ms_level << <span class="stringliteral">"\" peaksCount=\""</span></div>
<div class="line"><a name="l01129"></a><span class="lineno"> 1129</span>  << spec.size() << <span class="stringliteral">"\" polarity=\""</span>;</div>
<div class="line"><a name="l01130"></a><span class="lineno"> 1130</span>  <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a8f7be6e80ef1c4599af3aa096c7f7089">getPolarity</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054a03d440bbbfb042afc85347f994b44fb5">IonSource::POSITIVE</a>)</div>
<div class="line"><a name="l01131"></a><span class="lineno"> 1131</span>  {</div>
<div class="line"><a name="l01132"></a><span class="lineno"> 1132</span>  os << <span class="stringliteral">"+"</span>;</div>
<div class="line"><a name="l01133"></a><span class="lineno"> 1133</span>  }</div>
<div class="line"><a name="l01134"></a><span class="lineno"> 1134</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a8f7be6e80ef1c4599af3aa096c7f7089">getPolarity</a>() == <a class="code" href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054a62d66a51fa7574c652597716f7709865">IonSource::NEGATIVE</a>)</div>
<div class="line"><a name="l01135"></a><span class="lineno"> 1135</span>  {</div>
<div class="line"><a name="l01136"></a><span class="lineno"> 1136</span>  os << <span class="stringliteral">"-"</span>;</div>
<div class="line"><a name="l01137"></a><span class="lineno"> 1137</span>  }</div>
<div class="line"><a name="l01138"></a><span class="lineno"> 1138</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01139"></a><span class="lineno"> 1139</span>  {</div>
<div class="line"><a name="l01140"></a><span class="lineno"> 1140</span>  os << <span class="stringliteral">"any"</span>;</div>
<div class="line"><a name="l01141"></a><span class="lineno"> 1141</span>  }</div>
<div class="line"><a name="l01142"></a><span class="lineno"> 1142</span> </div>
<div class="line"><a name="l01143"></a><span class="lineno"> 1143</span>  <span class="comment">//scan type</span></div>
<div class="line"><a name="l01144"></a><span class="lineno"> 1144</span>  <span class="keywordflow">switch</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>())</div>
<div class="line"><a name="l01145"></a><span class="lineno"> 1145</span>  {</div>
<div class="line"><a name="l01146"></a><span class="lineno"> 1146</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a6ce26a62afab55d7606ad4e92428b30c">InstrumentSettings::UNKNOWN</a>:</div>
<div class="line"><a name="l01147"></a><span class="lineno"> 1147</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01148"></a><span class="lineno"> 1148</span> </div>
<div class="line"><a name="l01149"></a><span class="lineno"> 1149</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">InstrumentSettings::MASSSPECTRUM</a>:</div>
<div class="line"><a name="l01150"></a><span class="lineno"> 1150</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a9b884a7152aea2da5e9c85439678e5e9">InstrumentSettings::MS1SPECTRUM</a>:</div>
<div class="line"><a name="l01151"></a><span class="lineno"> 1151</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad1561b04e39806321c10bc90516e846d">InstrumentSettings::MSNSPECTRUM</a>:</div>
<div class="line"><a name="l01152"></a><span class="lineno"> 1152</span>  <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a3409c914db15bbb4696822e623a69ef1">getZoomScan</a>())</div>
<div class="line"><a name="l01153"></a><span class="lineno"> 1153</span>  {</div>
<div class="line"><a name="l01154"></a><span class="lineno"> 1154</span>  os << <span class="stringliteral">"\" scanType=\"zoom"</span>;</div>
<div class="line"><a name="l01155"></a><span class="lineno"> 1155</span>  }</div>
<div class="line"><a name="l01156"></a><span class="lineno"> 1156</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01157"></a><span class="lineno"> 1157</span>  {</div>
<div class="line"><a name="l01158"></a><span class="lineno"> 1158</span>  os << <span class="stringliteral">"\" scanType=\"Full"</span>;</div>
<div class="line"><a name="l01159"></a><span class="lineno"> 1159</span>  }</div>
<div class="line"><a name="l01160"></a><span class="lineno"> 1160</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01161"></a><span class="lineno"> 1161</span> </div>
<div class="line"><a name="l01162"></a><span class="lineno"> 1162</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746">InstrumentSettings::SIM</a>:</div>
<div class="line"><a name="l01163"></a><span class="lineno"> 1163</span>  os << <span class="stringliteral">"\" scanType=\"SIM"</span>;</div>
<div class="line"><a name="l01164"></a><span class="lineno"> 1164</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01165"></a><span class="lineno"> 1165</span> </div>
<div class="line"><a name="l01166"></a><span class="lineno"> 1166</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">InstrumentSettings::SRM</a>:</div>
<div class="line"><a name="l01167"></a><span class="lineno"> 1167</span>  os << <span class="stringliteral">"\" scanType=\"SRM"</span>;</div>
<div class="line"><a name="l01168"></a><span class="lineno"> 1168</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01169"></a><span class="lineno"> 1169</span> </div>
<div class="line"><a name="l01170"></a><span class="lineno"> 1170</span>  <span class="keywordflow">case</span> <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0af3d1715feea7314cc0ed1080191ea57d">InstrumentSettings::CRM</a>:</div>
<div class="line"><a name="l01171"></a><span class="lineno"> 1171</span>  os << <span class="stringliteral">"\" scanType=\"CRM"</span>;</div>
<div class="line"><a name="l01172"></a><span class="lineno"> 1172</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01173"></a><span class="lineno"> 1173</span> </div>
<div class="line"><a name="l01174"></a><span class="lineno"> 1174</span>  <span class="keywordflow">default</span>:</div>
<div class="line"><a name="l01175"></a><span class="lineno"> 1175</span>  os << <span class="stringliteral">"\" scanType=\"Full"</span>;</div>
<div class="line"><a name="l01176"></a><span class="lineno"> 1176</span>  warning(STORE, <a class="code" href="classOpenMS_1_1String.html">String</a>(<span class="stringliteral">"Scan type '"</span>) + <a class="code" href="classOpenMS_1_1InstrumentSettings.html#af9ecf94ffd05a020cce7a2d10794a192">InstrumentSettings::NamesOfScanMode</a>[spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">getScanMode</a>()] + <span class="stringliteral">"' not supported by mzXML. Using 'Full' scan mode!"</span>);</div>
<div class="line"><a name="l01177"></a><span class="lineno"> 1177</span>  }</div>
<div class="line"><a name="l01178"></a><span class="lineno"> 1178</span> </div>
<div class="line"><a name="l01179"></a><span class="lineno"> 1179</span>  os << <span class="stringliteral">"\" retentionTime=\""</span>;</div>
<div class="line"><a name="l01180"></a><span class="lineno"> 1180</span>  <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>() < 0)</div>
<div class="line"><a name="l01181"></a><span class="lineno"> 1181</span>  os << <span class="stringliteral">"-"</span>;</div>
<div class="line"><a name="l01182"></a><span class="lineno"> 1182</span>  os << <span class="stringliteral">"PT"</span> << std::fabs(spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">getRT</a>()) << <span class="stringliteral">"S\""</span>;</div>
<div class="line"><a name="l01183"></a><span class="lineno"> 1183</span>  <span class="keywordflow">if</span> (!spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>().empty())</div>
<div class="line"><a name="l01184"></a><span class="lineno"> 1184</span>  {</div>
<div class="line"><a name="l01185"></a><span class="lineno"> 1185</span>  os << <span class="stringliteral">" startMz=\""</span> << spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>()[0].begin << <span class="stringliteral">"\" endMz=\""</span> << spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>()[0].end << <span class="stringliteral">"\""</span>;</div>
<div class="line"><a name="l01186"></a><span class="lineno"> 1186</span>  }</div>
<div class="line"><a name="l01187"></a><span class="lineno"> 1187</span>  <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">getInstrumentSettings</a>().<a class="code" href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">getScanWindows</a>().size() > 1)</div>
<div class="line"><a name="l01188"></a><span class="lineno"> 1188</span>  {</div>
<div class="line"><a name="l01189"></a><span class="lineno"> 1189</span>  warning(STORE, <span class="stringliteral">"The MzXML format can store only one scan window for each scan. Only the first one is stored!"</span>);</div>
<div class="line"><a name="l01190"></a><span class="lineno"> 1190</span>  }</div>
<div class="line"><a name="l01191"></a><span class="lineno"> 1191</span>  os << <span class="stringliteral">">\n"</span>;</div>
<div class="line"><a name="l01192"></a><span class="lineno"> 1192</span> </div>
<div class="line"><a name="l01193"></a><span class="lineno"> 1193</span> </div>
<div class="line"><a name="l01194"></a><span class="lineno"> 1194</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">getPrecursors</a>().size(); ++i)</div>
<div class="line"><a name="l01195"></a><span class="lineno"> 1195</span>  {</div>
<div class="line"><a name="l01196"></a><span class="lineno"> 1196</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1Precursor.html">Precursor</a>& precursor = spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">getPrecursors</a>()[i];</div>
<div class="line"><a name="l01197"></a><span class="lineno"> 1197</span>  <span class="comment">//intensity</span></div>
<div class="line"><a name="l01198"></a><span class="lineno"> 1198</span>  os << <a class="code" href="classOpenMS_1_1String.html">String</a>(ms_level + 2, <span class="charliteral">'\t'</span>) << <span class="stringliteral">"<precursorMz precursorIntensity=\""</span> << precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#a09903c7965f8ece31f2c1e07b41ae6dd">getIntensity</a>();</div>
<div class="line"><a name="l01199"></a><span class="lineno"> 1199</span>  <span class="comment">//charge</span></div>
<div class="line"><a name="l01200"></a><span class="lineno"> 1200</span>  <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ab91109da6782d902c745c771aa85d03d">getCharge</a>() != 0)</div>
<div class="line"><a name="l01201"></a><span class="lineno"> 1201</span>  os << <span class="stringliteral">"\" precursorCharge=\""</span> << precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ab91109da6782d902c745c771aa85d03d">getCharge</a>();</div>
<div class="line"><a name="l01202"></a><span class="lineno"> 1202</span>  <span class="comment">//window size</span></div>
<div class="line"><a name="l01203"></a><span class="lineno"> 1203</span>  <span class="keywordflow">if</span> (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ac6f71e641c709dfabecce317d07ac4f7">getIsolationWindowLowerOffset</a>() != precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a0d3c115101baf89ff0d81602ad6cc635">getIsolationWindowUpperOffset</a>())</div>
<div class="line"><a name="l01204"></a><span class="lineno"> 1204</span>  os << <span class="stringliteral">"\" windowWideness=\""</span> << (precursor.<a class="code" href="classOpenMS_1_1Precursor.html#a0d3c115101baf89ff0d81602ad6cc635">getIsolationWindowUpperOffset</a>() - precursor.<a class="code" href="classOpenMS_1_1Precursor.html#ac6f71e641c709dfabecce317d07ac4f7">getIsolationWindowLowerOffset</a>());</div>
<div class="line"><a name="l01205"></a><span class="lineno"> 1205</span>  <span class="comment">//m/z</span></div>
<div class="line"><a name="l01206"></a><span class="lineno"> 1206</span>  os << <span class="stringliteral">"\">"</span> << precursor.<a class="code" href="classOpenMS_1_1Peak1D.html#a6fefef82aae7a3208e71648e763d5ea4">getMZ</a>() << <span class="stringliteral">"</precursorMz>\n"</span>;</div>
<div class="line"><a name="l01207"></a><span class="lineno"> 1207</span>  }</div>
<div class="line"><a name="l01208"></a><span class="lineno"> 1208</span> </div>
<div class="line"><a name="l01209"></a><span class="lineno"> 1209</span>  <span class="keywordflow">if</span> (!spec.empty())</div>
<div class="line"><a name="l01210"></a><span class="lineno"> 1210</span>  {</div>
<div class="line"><a name="l01211"></a><span class="lineno"> 1211</span>  os << <a class="code" href="classOpenMS_1_1String.html">String</a>(ms_level + 2, <span class="charliteral">'\t'</span>) << <span class="stringliteral">"<peaks precision=\"32\""</span> << <span class="stringliteral">" byteOrder=\"network\" pairOrder=\"m/z-int\">"</span>;</div>
<div class="line"><a name="l01212"></a><span class="lineno"> 1212</span> </div>
<div class="line"><a name="l01213"></a><span class="lineno"> 1213</span>  <span class="comment">//std::cout << "Writing scan " << s << "\n";</span></div>
<div class="line"><a name="l01214"></a><span class="lineno"> 1214</span>  std::vector<Real> tmp;</div>
<div class="line"><a name="l01215"></a><span class="lineno"> 1215</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < spec.size(); i++)</div>
<div class="line"><a name="l01216"></a><span class="lineno"> 1216</span>  {</div>
<div class="line"><a name="l01217"></a><span class="lineno"> 1217</span>  tmp.push_back(spec[i].getMZ());</div>
<div class="line"><a name="l01218"></a><span class="lineno"> 1218</span>  tmp.push_back(spec[i].getIntensity());</div>
<div class="line"><a name="l01219"></a><span class="lineno"> 1219</span>  }</div>
<div class="line"><a name="l01220"></a><span class="lineno"> 1220</span> </div>
<div class="line"><a name="l01221"></a><span class="lineno"> 1221</span>  <a class="code" href="classOpenMS_1_1String.html">String</a> encoded;</div>
<div class="line"><a name="l01222"></a><span class="lineno"> 1222</span>  decoder_.encode(tmp, <a class="code" href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142ba6e7bcd2266b848fe3284e93c291c42b4">Base64::BYTEORDER_BIGENDIAN</a>, encoded);</div>
<div class="line"><a name="l01223"></a><span class="lineno"> 1223</span>  os << encoded << <span class="stringliteral">"</peaks>\n"</span>;</div>
<div class="line"><a name="l01224"></a><span class="lineno"> 1224</span>  }</div>
<div class="line"><a name="l01225"></a><span class="lineno"> 1225</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l01226"></a><span class="lineno"> 1226</span>  {</div>
<div class="line"><a name="l01227"></a><span class="lineno"> 1227</span>  os << <a class="code" href="classOpenMS_1_1String.html">String</a>(ms_level + 2, <span class="charliteral">'\t'</span>) << <span class="stringliteral">"<peaks precision=\"32\""</span> << <span class="stringliteral">" byteOrder=\"network\" pairOrder=\"m/z-int\" xsi:nil=\"true\"/>\n"</span>;</div>
<div class="line"><a name="l01228"></a><span class="lineno"> 1228</span>  }</div>
<div class="line"><a name="l01229"></a><span class="lineno"> 1229</span> </div>
<div class="line"><a name="l01230"></a><span class="lineno"> 1230</span>  writeUserParam_(os, spec, ms_level + 2);</div>
<div class="line"><a name="l01231"></a><span class="lineno"> 1231</span>  <span class="keywordflow">if</span> (spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#af974151b7df6fcfeb6509e26431dcaa0">getComment</a>() != <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l01232"></a><span class="lineno"> 1232</span>  {</div>
<div class="line"><a name="l01233"></a><span class="lineno"> 1233</span>  os << <a class="code" href="classOpenMS_1_1String.html">String</a>(ms_level + 2, <span class="charliteral">'\t'</span>) << <span class="stringliteral">"<comment>"</span> << spec.<a class="code" href="classOpenMS_1_1SpectrumSettings.html#af974151b7df6fcfeb6509e26431dcaa0">getComment</a>() << <span class="stringliteral">"</comment>\n"</span>;</div>
<div class="line"><a name="l01234"></a><span class="lineno"> 1234</span>  }</div>
<div class="line"><a name="l01235"></a><span class="lineno"> 1235</span> </div>
<div class="line"><a name="l01236"></a><span class="lineno"> 1236</span>  <span class="comment">//check MS level of next scan and close scans (scans can be nested)</span></div>
<div class="line"><a name="l01237"></a><span class="lineno"> 1237</span>  <a class="code" href="classunsigned_01int.html">UInt</a> next_ms_level = 0;</div>
<div class="line"><a name="l01238"></a><span class="lineno"> 1238</span>  <span class="keywordflow">if</span> (s < cexp_->size() - 1)</div>
<div class="line"><a name="l01239"></a><span class="lineno"> 1239</span>  {</div>
<div class="line"><a name="l01240"></a><span class="lineno"> 1240</span>  next_ms_level = ((*cexp_)[s + 1]).getMSLevel();</div>
<div class="line"><a name="l01241"></a><span class="lineno"> 1241</span>  }</div>
<div class="line"><a name="l01242"></a><span class="lineno"> 1242</span>  <span class="comment">//std::cout << "scan: " << s << " this: " << ms_level << " next: " << next_ms_level << "\n";</span></div>
<div class="line"><a name="l01243"></a><span class="lineno"> 1243</span>  <span class="keywordflow">if</span> (next_ms_level <= ms_level)</div>
<div class="line"><a name="l01244"></a><span class="lineno"> 1244</span>  {</div>
<div class="line"><a name="l01245"></a><span class="lineno"> 1245</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i <= ms_level - next_ms_level && !open_scans.empty(); ++i)</div>
<div class="line"><a name="l01246"></a><span class="lineno"> 1246</span>  {</div>
<div class="line"><a name="l01247"></a><span class="lineno"> 1247</span>  os << <a class="code" href="classOpenMS_1_1String.html">String</a>(ms_level - i + 1, <span class="charliteral">'\t'</span>) << <span class="stringliteral">"</scan>\n"</span>;</div>
<div class="line"><a name="l01248"></a><span class="lineno"> 1248</span>  open_scans.pop();</div>
<div class="line"><a name="l01249"></a><span class="lineno"> 1249</span>  }</div>
<div class="line"><a name="l01250"></a><span class="lineno"> 1250</span>  }</div>
<div class="line"><a name="l01251"></a><span class="lineno"> 1251</span>  }</div>
<div class="line"><a name="l01252"></a><span class="lineno"> 1252</span> </div>
<div class="line"><a name="l01253"></a><span class="lineno"> 1253</span>  os << <span class="stringliteral">"\t</msRun>\n"</span></div>
<div class="line"><a name="l01254"></a><span class="lineno"> 1254</span>  << <span class="stringliteral">"\t<indexOffset>0</indexOffset>\n"</span></div>
<div class="line"><a name="l01255"></a><span class="lineno"> 1255</span>  << <span class="stringliteral">"</mzXML>\n"</span>;</div>
<div class="line"><a name="l01256"></a><span class="lineno"> 1256</span> </div>
<div class="line"><a name="l01257"></a><span class="lineno"> 1257</span>  logger_.endProgress();</div>
<div class="line"><a name="l01258"></a><span class="lineno"> 1258</span>  spec_write_counter_ = 1;</div>
<div class="line"><a name="l01259"></a><span class="lineno"> 1259</span>  }</div>
<div class="line"><a name="l01260"></a><span class="lineno"> 1260</span> </div>
<div class="line"><a name="l01261"></a><span class="lineno"> 1261</span>  } <span class="comment">// namespace Internal</span></div>
<div class="line"><a name="l01262"></a><span class="lineno"> 1262</span> </div>
<div class="line"><a name="l01263"></a><span class="lineno"> 1263</span> } <span class="comment">// namespace OpenMS</span></div>
<div class="line"><a name="l01264"></a><span class="lineno"> 1264</span> </div>
<div class="line"><a name="l01265"></a><span class="lineno"> 1265</span> <span class="preprocessor">#endif</span></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9a1491834ae41afad2cd5d4e69f20aaaae"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a1491834ae41afad2cd5d4e69f20aaaae">OpenMS::DataProcessing::DEISOTOPING</a></div><div class="ttdoc">Deisotoping. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_aae35ae2dfad88d673b03c787aafca83d"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#aae35ae2dfad88d673b03c787aafca83d">OpenMS::MetaInfoInterface::getMetaValue</a></div><div class="ttdeci">const DataValue & getMetaValue(const String &name) const </div><div class="ttdoc">returns the value corresponding to a string </div></div>
<div class="ttc" id="PeakFileOptions_8h_html"><div class="ttname"><a href="PeakFileOptions_8h.html">PeakFileOptions.h</a></div></div>
<div class="ttc" id="classunsigned_01int_html"><div class="ttname"><a href="classunsigned_01int.html">unsigned int</a></div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html">OpenMS::DataProcessing</a></div><div class="ttdoc">Descripton of the applied preprocessing steps. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_aec2ce57bef42db3fc6b2df2b3d3c9e6a"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aec2ce57bef42db3fc6b2df2b3d3c9e6a">OpenMS::Internal::MzXMLHandler::compressionType_</a></div><div class="ttdeci">String compressionType_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:181</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_a2bf1ca8186169631f23edd67ddbd45e1"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#a2bf1ca8186169631f23edd67ddbd45e1">OpenMS::SourceFile::getChecksumType</a></div><div class="ttdeci">ChecksumType getChecksumType() const </div><div class="ttdoc">returns the checksum type </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_acecccc91c6a09c5814ee7f4923a53b3d"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#acecccc91c6a09c5814ee7f4923a53b3d">OpenMS::Internal::MzXMLHandler::writeUserParam_</a></div><div class="ttdeci">void writeUserParam_(std::ostream &os, const MetaInfoInterface &meta, int indent=4, String tag="nameValue")</div><div class="ttdoc">write metaInfo to xml (usually in nameValue-tag) </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:195</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4afca6a564be564def43e05f3204a973e3"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4afca6a564be564def43e05f3204a973e3">OpenMS::IonSource::SIZE_OF_IONIZATIONMETHOD</a></div><div class="ttdef"><b>Definition:</b> IonSource.h:134</div></div>
<div class="ttc" id="classOpenMS_1_1Base64_html_aaeb92d42f5a6e27b8ba19f18d69d142ba6e7bcd2266b848fe3284e93c291c42b4"><div class="ttname"><a href="classOpenMS_1_1Base64.html#aaeb92d42f5a6e27b8ba19f18d69d142ba6e7bcd2266b848fe3284e93c291c42b4">OpenMS::Base64::BYTEORDER_BIGENDIAN</a></div><div class="ttdoc">Big endian type. </div><div class="ttdef"><b>Definition:</b> Base64.h:78</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html"><div class="ttname"><a href="classOpenMS_1_1Instrument.html">OpenMS::Instrument</a></div><div class="ttdoc">Description of a MS instrument. </div><div class="ttdef"><b>Definition:</b> Instrument.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_acadddeff186604f0185315e70aab94fb"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#acadddeff186604f0185315e70aab94fb">OpenMS::SourceFile::getNameOfFile</a></div><div class="ttdeci">const String & getNameOfFile() const </div><div class="ttdoc">returns the file name </div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_a219795d06917877c7d946a00f23e2319"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#a219795d06917877c7d946a00f23e2319">OpenMS::Instrument::getSoftware</a></div><div class="ttdeci">const Software & getSoftware() const </div><div class="ttdoc">returns a const reference to the instrument software </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_ae9e005976a3adc6ee08cc2d3dcfa3051"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae9e005976a3adc6ee08cc2d3dcfa3051">OpenMS::Internal::MzXMLHandler::s_count_</a></div><div class="ttdeci">static const XMLCh * s_count_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:217</div></div>
<div class="ttc" id="classOpenMS_1_1String_html"><div class="ttname"><a href="classOpenMS_1_1String.html">OpenMS::String</a></div><div class="ttdoc">A more convenient string class. </div><div class="ttdef"><b>Definition:</b> String.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html"><div class="ttname"><a href="classOpenMS_1_1Precursor.html">OpenMS::Precursor</a></div><div class="ttdoc">Precursor meta information. </div><div class="ttdef"><b>Definition:</b> Precursor.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1Base64_html"><div class="ttname"><a href="classOpenMS_1_1Base64.html">OpenMS::Base64</a></div><div class="ttdoc">Class to encode and decode Base64. </div><div class="ttdef"><b>Definition:</b> Base64.h:64</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a11010cea213654791e0211426489563b"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a11010cea213654791e0211426489563b">OpenMS::Internal::MzXMLHandler::precision_</a></div><div class="ttdeci">String precision_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:180</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_1_1EndParsingSoftly_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler_1_1EndParsingSoftly.html">OpenMS::Internal::XMLHandler::EndParsingSoftly</a></div><div class="ttdoc">Exception that is thrown if the parsing is ended by some event (e.g. if only a prefix of the XML file...</div><div class="ttdef"><b>Definition:</b> XMLHandler.h:94</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_a80c69c45fa9891b7de1229a3ff53f468"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#a80c69c45fa9891b7de1229a3ff53f468">OpenMS::Instrument::getIonSources</a></div><div class="ttdeci">const std::vector< IonSource > & getIonSources() const </div><div class="ttdoc">returns a const reference to the ion source list </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a538550ae672ce0c5aa5a6e2b45688e9e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a538550ae672ce0c5aa5a6e2b45688e9e">OpenMS::Internal::MzXMLHandler::s_peakscount_</a></div><div class="ttdeci">static const XMLCh * s_peakscount_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:233</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a1726d12d7597baa9fca0c1da0492f3da"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a1726d12d7597baa9fca0c1da0492f3da">OpenMS::MSSpectrum::getMSLevel</a></div><div class="ttdeci">UInt getMSLevel() const </div><div class="ttdoc">Returns the MS level. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:231</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a5a8077778dc3c534832ee1a3d79e9e72"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5a8077778dc3c534832ee1a3d79e9e72">OpenMS::Internal::MzXMLHandler::s_name_</a></div><div class="ttdeci">static const XMLCh * s_name_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:219</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a11053909f1f8edf7b9ccc41c1417ecf6a143a6a9882aaf613c6f529b976da6eea"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a11053909f1f8edf7b9ccc41c1417ecf6a143a6a9882aaf613c6f529b976da6eea">OpenMS::MassAnalyzer::SIZE_OF_RESOLUTIONMETHOD</a></div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:86</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_a09903c7965f8ece31f2c1e07b41ae6dd"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#a09903c7965f8ece31f2c1e07b41ae6dd">OpenMS::Peak1D::getIntensity</a></div><div class="ttdeci">IntensityType getIntensity() const </div><div class="ttdef"><b>Definition:</b> Peak1D.h:103</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_aa4a976a043fd323d6241a0e6a82274d9"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aa4a976a043fd323d6241a0e6a82274d9">OpenMS::Internal::MzXMLHandler::s_first_</a></div><div class="ttdeci">static const XMLCh * s_first_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:239</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_ac7f1dc19152ee580c397658d088a6a4f"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ac7f1dc19152ee580c397658d088a6a4f">OpenMS::Internal::MzXMLHandler::s_phone_</a></div><div class="ttdeci">static const XMLCh * s_phone_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:241</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a3bcdda3510d6f4c85d3e3669fe044946"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a3bcdda3510d6f4c85d3e3669fe044946">OpenMS::Internal::MzXMLHandler::s_centroided_</a></div><div class="ttdeci">static const XMLCh * s_centroided_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:246</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a1d9a2d74c791b49639ee41852966f0a3"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a1d9a2d74c791b49639ee41852966f0a3">OpenMS::Internal::MzXMLHandler::spec_write_counter_</a></div><div class="ttdeci">UInt spec_write_counter_</div><div class="ttdoc">spectrum counter (spectra without peaks are not written) </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:189</div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_ad34bb2f8f677e2f6c6c505d11754a765"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#ad34bb2f8f677e2f6c6c505d11754a765">OpenMS::DataProcessing::getProcessingActions</a></div><div class="ttdeci">const std::set< ProcessingAction > & getProcessingActions() const </div><div class="ttdoc">returns a const reference to the applied processing actions </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a372aba127092cba03b2745c3bd71dcd2"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a372aba127092cba03b2745c3bd71dcd2">OpenMS::Internal::MzXMLHandler::s_precursorcharge_</a></div><div class="ttdeci">static const XMLCh * s_precursorcharge_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:230</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a00d2844792e6c6f7ad3fe2c46201a57a"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a00d2844792e6c6f7ad3fe2c46201a57a">OpenMS::Internal::MzXMLHandler::s_filesha1_</a></div><div class="ttdeci">static const XMLCh * s_filesha1_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:223</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a2b299003c15ddc54383dec1745f54944"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a2b299003c15ddc54383dec1745f54944">OpenMS::Internal::MzXMLHandler::PeakIterator</a></div><div class="ttdeci">SpectrumType::Iterator PeakIterator</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:166</div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html">OpenMS::ContactPerson</a></div><div class="ttdoc">Contact person information. </div><div class="ttdef"><b>Definition:</b> ContactPerson.h:50</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_af974151b7df6fcfeb6509e26431dcaa0"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#af974151b7df6fcfeb6509e26431dcaa0">OpenMS::SpectrumSettings::getComment</a></div><div class="ttdeci">const String & getComment() const </div><div class="ttdoc">returns the free-text comment </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a84a045fa4024e050ca8be6d33311a054a62d66a51fa7574c652597716f7709865"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054a62d66a51fa7574c652597716f7709865">OpenMS::IonSource::NEGATIVE</a></div><div class="ttdoc">Negative polarity. </div><div class="ttdef"><b>Definition:</b> IonSource.h:144</div></div>
<div class="ttc" id="ProgressLogger_8h_html"><div class="ttname"><a href="ProgressLogger_8h.html">ProgressLogger.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_af3feca15695c5ad09a91b35d43559e57"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#af3feca15695c5ad09a91b35d43559e57">OpenMS::Instrument::getMassAnalyzers</a></div><div class="ttdeci">const std::vector< MassAnalyzer > & getMassAnalyzers() const </div><div class="ttdoc">returns a const reference to the mass analyer list </div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html_a82e960f65e28ae6aba1271adbb83236e"><div class="ttname"><a href="classOpenMS_1_1DataValue.html#a82e960f65e28ae6aba1271adbb83236e">OpenMS::DataValue::toString</a></div><div class="ttdeci">String toString() const </div><div class="ttdoc">Conversion to String. </div></div>
<div class="ttc" id="structOpenMS_1_1ScanWindow_html_aed18ab075b5c0317ae32335a57f899e8"><div class="ttname"><a href="structOpenMS_1_1ScanWindow.html#aed18ab075b5c0317ae32335a57f899e8">OpenMS::ScanWindow::end</a></div><div class="ttdeci">DoubleReal end</div><div class="ttdoc">End of the window. </div><div class="ttdef"><b>Definition:</b> ScanWindow.h:64</div></div>
<div class="ttc" id="namespaceOpenMS_html_a013338b7bdbb5c3b4c78666656070e23"><div class="ttname"><a href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">OpenMS::PeakType</a></div><div class="ttdeci">Peak2D PeakType</div><div class="ttdef"><b>Definition:</b> MassTrace.h:49</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_a2d47bfad02d5ce05dcfab38bc1b21400"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#a2d47bfad02d5ce05dcfab38bc1b21400">OpenMS::SourceFile::setFileType</a></div><div class="ttdeci">void setFileType(const String &file_type)</div><div class="ttdoc">sets the file type </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html">OpenMS::Internal::MzXMLHandler</a></div><div class="ttdoc">XML handlers for MzXMLFile. </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1Peak1D_html_a6fefef82aae7a3208e71648e763d5ea4"><div class="ttname"><a href="classOpenMS_1_1Peak1D.html#a6fefef82aae7a3208e71648e763d5ea4">OpenMS::Peak1D::getMZ</a></div><div class="ttdeci">CoordinateType getMZ() const </div><div class="ttdoc">Non-mutable access to m/z. </div><div class="ttdef"><b>Definition:</b> Peak1D.h:108</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a84a045fa4024e050ca8be6d33311a054a03d440bbbfb042afc85347f994b44fb5"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054a03d440bbbfb042afc85347f994b44fb5">OpenMS::IonSource::POSITIVE</a></div><div class="ttdoc">Positive polarity. </div><div class="ttdef"><b>Definition:</b> IonSource.h:143</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3a7925ff36af091300c66ad1f9615dbdc6"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3a7925ff36af091300c66ad1f9615dbdc6">OpenMS::MassAnalyzer::SIZE_OF_ANALYZERTYPE</a></div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:70</div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ab91109da6782d902c745c771aa85d03d"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ab91109da6782d902c745c771aa85d03d">OpenMS::Precursor::getCharge</a></div><div class="ttdeci">Int getCharge() const </div><div class="ttdoc">Non-mutable access to the charge. </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_aa1612242e2b5ea583324fadd8f0e5198"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aa1612242e2b5ea583324fadd8f0e5198">OpenMS::Internal::MzXMLHandler::startElement</a></div><div class="ttdeci">virtual void startElement(const XMLCh *const uri, const XMLCh *const local_name, const XMLCh *const qname, const xercesc::Attributes &attributes)</div><div class="ttdoc">Parsing method for opening tags. </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:368</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_html"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html">OpenMS::Internal::XMLHandler</a></div><div class="ttdoc">Base class for XML handlers. </div><div class="ttdef"><b>Definition:</b> XMLHandler.h:89</div></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_a796a6cd8072195dfaf282a0827bebb4a"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#a796a6cd8072195dfaf282a0827bebb4a">OpenMS::Instrument::getIonDetectors</a></div><div class="ttdeci">const std::vector< IonDetector > & getIonDetectors() const </div><div class="ttdoc">returns a const reference to the ion detector list </div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html">OpenMS::SourceFile</a></div><div class="ttdoc">Description of a file location, used to store the origin of (meta) data. </div><div class="ttdef"><b>Definition:</b> SourceFile.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_ae58d7d4470df102db1bc01dfb2adaa07"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae58d7d4470df102db1bc01dfb2adaa07">OpenMS::Internal::MzXMLHandler::s_retentiontime_</a></div><div class="ttdeci">static const XMLCh * s_retentiontime_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:236</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_html_a2f223274d440404ba700768cd15ef661"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html#a2f223274d440404ba700768cd15ef661">OpenMS::Internal::XMLHandler::XMLHandler</a></div><div class="ttdeci">XMLHandler()</div><div class="ttdoc">Not implemented. </div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a58599d37159ebc08a654fb2d25be92fe"><div class="ttname"><a href="classOpenMS_1_1String.html#a58599d37159ebc08a654fb2d25be92fe">OpenMS::String::has</a></div><div class="ttdeci">bool has(Byte byte) const </div><div class="ttdoc">true if String contains the byte, false otherwise </div></div>
<div class="ttc" id="structOpenMS_1_1ScanWindow_html_aea3ca80628c489842c52a61e195dd047"><div class="ttname"><a href="structOpenMS_1_1ScanWindow.html#aea3ca80628c489842c52a61e195dd047">OpenMS::ScanWindow::begin</a></div><div class="ttdeci">DoubleReal begin</div><div class="ttdoc">Begin of the window. </div><div class="ttdef"><b>Definition:</b> ScanWindow.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0ad1561b04e39806321c10bc90516e846d"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad1561b04e39806321c10bc90516e846d">OpenMS::InstrumentSettings::MSNSPECTRUM</a></div><div class="ttdoc">MS2+ mass spectrum, is a &quot;mass spectrum&quot;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:58</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a6d64276a665c3c0dca8fb4ade3c8b477"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a6d64276a665c3c0dca8fb4ade3c8b477">OpenMS::MSSpectrum< PeakType >::Iterator</a></div><div class="ttdeci">ContainerType::iterator Iterator</div><div class="ttdoc">Mutable iterator. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:123</div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7">OpenMS::IonDetector::Type</a></div><div class="ttdeci">Type</div><div class="ttdoc">Detector type. </div><div class="ttdef"><b>Definition:</b> IonDetector.h:52</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a1a8726a589fa6c4c96b4db825abf8a4b">OpenMS::InstrumentSettings::SRM</a></div><div class="ttdoc">Selected reaction monitoring scan Synonyms: &#39;Multiple reaction monitoring scan&#39;, &#39;SRM scan&#39;, &#39;MRM scan&#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:60</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_affa32793fdd4f1526a6c34c17626a60a"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#affa32793fdd4f1526a6c34c17626a60a">OpenMS::SourceFile::setChecksum</a></div><div class="ttdeci">void setChecksum(const String &checksum, ChecksumType type)</div><div class="ttdoc">sets the file&#39;s checksum </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_ad8f6ee9d6ad9dd9642c5f25864288ff0"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ad8f6ee9d6ad9dd9642c5f25864288ff0">OpenMS::Internal::MzXMLHandler::s_scantype_</a></div><div class="ttdeci">static const XMLCh * s_scantype_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:235</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_ae19606cee74ec0ac3662fcfba274cbd0"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae19606cee74ec0ac3662fcfba274cbd0">OpenMS::Internal::MzXMLHandler::cexp_</a></div><div class="ttdeci">const MapType * cexp_</div><div class="ttdoc">map pointer for writing </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:171</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_a3409c914db15bbb4696822e623a69ef1"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#a3409c914db15bbb4696822e623a69ef1">OpenMS::InstrumentSettings::getZoomScan</a></div><div class="ttdeci">bool getZoomScan() const </div><div class="ttdoc">return if this scan is a zoom (enhanced resolution) scan </div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_a541856069e66db2a4cab95d7f1993dc9"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#a541856069e66db2a4cab95d7f1993dc9">OpenMS::InstrumentSettings::getScanMode</a></div><div class="ttdeci">ScanMode getScanMode() const </div><div class="ttdoc">returns the scan mode </div></div>
<div class="ttc" id="classOpenMS_1_1IonDetector_html_a1d1cfd8ffb84e947f82999c682b666a7a441c9a986459d5abed57acdcb0899409"><div class="ttname"><a href="classOpenMS_1_1IonDetector.html#a1d1cfd8ffb84e947f82999c682b666a7a441c9a986459d5abed57acdcb0899409">OpenMS::IonDetector::SIZE_OF_TYPE</a></div><div class="ttdef"><b>Definition:</b> IonDetector.h:76</div></div>
<div class="ttc" id="classOpenMS_1_1DateTime_html_ae8d3cac5cd5763984d9ca84d3453ed28"><div class="ttname"><a href="classOpenMS_1_1DateTime.html#ae8d3cac5cd5763984d9ca84d3453ed28">OpenMS::DateTime::get</a></div><div class="ttdeci">void get(UInt &month, UInt &day, UInt &year, UInt &hour, UInt &minute, UInt &second) const </div><div class="ttdoc">Fills the arguments with the date and the time. </div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a11053909f1f8edf7b9ccc41c1417ecf6"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a11053909f1f8edf7b9ccc41c1417ecf6">OpenMS::MassAnalyzer::ResolutionMethod</a></div><div class="ttdeci">ResolutionMethod</div><div class="ttdoc">resolution method </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:80</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a9c58f650dc7adebf723a67fdf07e9b87"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a9c58f650dc7adebf723a67fdf07e9b87">OpenMS::Internal::MzXMLHandler::s_polarity_</a></div><div class="ttdeci">static const XMLCh * s_polarity_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:234</div></div>
<div class="ttc" id="MSExperiment_8h_html"><div class="ttname"><a href="MSExperiment_8h.html">MSExperiment.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_ab0e6ea8a2659622ef3bcd7da7ce4a22c"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ab0e6ea8a2659622ef3bcd7da7ce4a22c">OpenMS::Internal::MzXMLHandler::~MzXMLHandler</a></div><div class="ttdeci">virtual ~MzXMLHandler()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:97</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< PeakType ></a></div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a28f849a39a6e1a02a891d9e7e7f6eb79"><div class="ttname"><a href="classOpenMS_1_1String.html#a28f849a39a6e1a02a891d9e7e7f6eb79">OpenMS::String::toInt</a></div><div class="ttdeci">Int toInt() const </div><div class="ttdoc">Conversion to int. </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a009a30591b3297275a4db1359fcd82ed"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a009a30591b3297275a4db1359fcd82ed">OpenMS::Internal::MzXMLHandler::init_</a></div><div class="ttdeci">void init_()</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:123</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_a021f6acb8bd3a02278cc50f11c489a12"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#a021f6acb8bd3a02278cc50f11c489a12">OpenMS::InstrumentSettings::getScanWindows</a></div><div class="ttdeci">const std::vector< ScanWindow > & getScanWindows() const </div><div class="ttdoc">returns a const reference to the m/z scan windows </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a4cd969d50e859e07ce2891b598a9a170"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4cd969d50e859e07ce2891b598a9a170">OpenMS::Internal::MzXMLHandler::s_byteorder_</a></div><div class="ttdeci">static const XMLCh * s_byteorder_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:226</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_ab4f6647bb6022332bcd7fbeadd0201b5"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ab4f6647bb6022332bcd7fbeadd0201b5">OpenMS::Internal::MzXMLHandler::s_completiontime_</a></div><div class="ttdeci">static const XMLCh * s_completiontime_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:224</div></div>
<div class="ttc" id="classOpenMS_1_1DPosition_html"><div class="ttname"><a href="classOpenMS_1_1DPosition.html">OpenMS::DPosition< 1 ></a></div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a8fd5f3c864af3d60885cc09888dd18d3"><div class="ttname"><a href="classOpenMS_1_1String.html#a8fd5f3c864af3d60885cc09888dd18d3">OpenMS::String::toLower</a></div><div class="ttdeci">String & toLower()</div><div class="ttdoc">Converts the string to lowercase. </div></div>
<div class="ttc" id="classOpenMS_1_1String_html_ad0f3113f29d5d2ebdfa090bab2cef7ac"><div class="ttname"><a href="classOpenMS_1_1String.html#ad0f3113f29d5d2ebdfa090bab2cef7ac">OpenMS::String::hasSubstring</a></div><div class="ttdeci">bool hasSubstring(const String &string) const </div><div class="ttdoc">true if String contains the string, false otherwise </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a654a0b5941d937e303c64bc9e732baec"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a654a0b5941d937e303c64bc9e732baec">OpenMS::Internal::MzXMLHandler::options_</a></div><div class="ttdeci">PeakFileOptions options_</div><div class="ttdoc">Options for loading and storing. </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:174</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a6cc33a53f7b3712dd7102b572434d0cf"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a6cc33a53f7b3712dd7102b572434d0cf">OpenMS::Internal::MzXMLHandler::s_num_</a></div><div class="ttdeci">static const XMLCh * s_num_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:244</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_a307ba40c92040f24cb0b496fb5b58b88"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#a307ba40c92040f24cb0b496fb5b58b88">OpenMS::Instrument::getModel</a></div><div class="ttdeci">const String & getModel() const </div><div class="ttdoc">returns the instrument model </div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a86864c88ee12eb322f1645f238c1dbe5"><div class="ttname"><a href="classOpenMS_1_1String.html#a86864c88ee12eb322f1645f238c1dbe5">OpenMS::String::trim</a></div><div class="ttdeci">String & trim()</div><div class="ttdoc">removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...</div></div>
<div class="ttc" id="structOpenMS_1_1ScanWindow_html"><div class="ttname"><a href="structOpenMS_1_1ScanWindow.html">OpenMS::ScanWindow</a></div><div class="ttdoc">Scan window description. </div><div class="ttdef"><b>Definition:</b> ScanWindow.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1Instrument_html_adeb3a96bea31dcca5dc2cba4d6e22cb5"><div class="ttname"><a href="classOpenMS_1_1Instrument.html#adeb3a96bea31dcca5dc2cba4d6e22cb5">OpenMS::Instrument::getVendor</a></div><div class="ttdeci">const String & getVendor() const </div><div class="ttdoc">returns the instrument vendor </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_ae22f2dafc17fa5b139b6805a58a01b67"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ae22f2dafc17fa5b139b6805a58a01b67">OpenMS::Internal::MzXMLHandler::char_rest_</a></div><div class="ttdeci">String char_rest_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:182</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a2d6d13f6b8cb30e7943d4996e9ef2af7"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a2d6d13f6b8cb30e7943d4996e9ef2af7">OpenMS::Internal::MzXMLHandler::setOptions</a></div><div class="ttdeci">void setOptions(const PeakFileOptions &options)</div><div class="ttdoc">Sets the options. </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:116</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a17154457c4614528cb46d566d022544b"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a17154457c4614528cb46d566d022544b">OpenMS::Internal::MzXMLHandler::s_value_</a></div><div class="ttdeci">static const XMLCh * s_value_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:216</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a9b884a7152aea2da5e9c85439678e5e9"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a9b884a7152aea2da5e9c85439678e5e9">OpenMS::InstrumentSettings::MS1SPECTRUM</a></div><div class="ttdoc">full scan mass spectrum, is a &quot;mass spectrum&quot; Synonyms: &#39;full spectrum&#39;, &#39;Q1 spectrum&#39;, &#39;Q3 spectrum&#39;, &#39;Single-Stage Mass Spectrometry&#39; </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_aaefa2a4a5d50f899cdd82d686104d164"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#aaefa2a4a5d50f899cdd82d686104d164">OpenMS::MetaInfoInterface::getKeys</a></div><div class="ttdeci">void getKeys(std::vector< String > &keys) const </div><div class="ttdoc">fills the given vector with a list of all keys for which a value is set </div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_a0d3c115101baf89ff0d81602ad6cc635"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#a0d3c115101baf89ff0d81602ad6cc635">OpenMS::Precursor::getIsolationWindowUpperOffset</a></div><div class="ttdeci">DoubleReal getIsolationWindowUpperOffset() const </div><div class="ttdoc">returns the upper offset from the target m/z </div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_a219795d06917877c7d946a00f23e2319"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#a219795d06917877c7d946a00f23e2319">OpenMS::DataProcessing::getSoftware</a></div><div class="ttdeci">const Software & getSoftware() const </div><div class="ttdoc">returns a const reference to the software used for processing </div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_aa1f350d16338b42e2384db2e5aa4a3f4"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#aa1f350d16338b42e2384db2e5aa4a3f4">OpenMS::IonSource::IonizationMethod</a></div><div class="ttdeci">IonizationMethod</div><div class="ttdoc">ionization method </div><div class="ttdef"><b>Definition:</b> IonSource.h:80</div></div>
<div class="ttc" id="classOpenMS_1_1Software_html_aaee0f2845288173de9f6ad47e6ad31d5"><div class="ttname"><a href="classOpenMS_1_1Software.html#aaee0f2845288173de9f6ad47e6ad31d5">OpenMS::Software::getName</a></div><div class="ttdeci">const String & getName() const </div><div class="ttdoc">returns the name of the software </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a7d4d4c968dc72284a6c9bfbdcde40b68"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a7d4d4c968dc72284a6c9bfbdcde40b68">OpenMS::Internal::MzXMLHandler::s_pairorder_</a></div><div class="ttdeci">static const XMLCh * s_pairorder_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:227</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0ad04d7145337b4c602725c632a0cf1746">OpenMS::InstrumentSettings::SIM</a></div><div class="ttdoc">Selected ion monitoring scan Synonyms: &#39;Multiple ion monitoring scan&#39;, &#39;SIM scan&#39;, &#39;MIM scan&#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:59</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a189e2aea7a4b8bbfcefbf62176d0966c"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a189e2aea7a4b8bbfcefbf62176d0966c">OpenMS::Internal::MzXMLHandler::peak_count_</a></div><div class="ttdeci">UInt peak_count_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:179</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html">OpenMS::MetaInfoInterface</a></div><div class="ttdoc">Interface for classes that can store arbitrary meta information (Type-Name-Value tuples). </div><div class="ttdef"><b>Definition:</b> MetaInfoInterface.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a50a6b2cdb2828e1f3e29c0096fd4ef63"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a50a6b2cdb2828e1f3e29c0096fd4ef63">OpenMS::Internal::MzXMLHandler::data_processing_</a></div><div class="ttdeci">std::vector< DataProcessing > data_processing_</div><div class="ttdoc">data processing auxilary variable </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:210</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1ConversionError_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1ConversionError.html">OpenMS::Exception::ConversionError</a></div><div class="ttdoc">Invalid conversion exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:363</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_af0a7eddbacf20c4f4045b671df6b0fe7"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#af0a7eddbacf20c4f4045b671df6b0fe7">OpenMS::SourceFile::setNameOfFile</a></div><div class="ttdeci">void setNameOfFile(const String &name_of_file)</div><div class="ttdoc">sets the file name </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a5e48b11d87737bed51dd492038c41279"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5e48b11d87737bed51dd492038c41279">OpenMS::Internal::MzXMLHandler::s_version_</a></div><div class="ttdeci">static const XMLCh * s_version_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:220</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_ac82b3cc3ba4c24b0ab9768fede8c3c9c"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#ac82b3cc3ba4c24b0ab9768fede8c3c9c">OpenMS::SourceFile::getFileType</a></div><div class="ttdeci">const String & getFileType() const </div><div class="ttdoc">returns the file type </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a6af0ff50dcb5a916e4cafba2b8f1d884"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a6af0ff50dcb5a916e4cafba2b8f1d884">OpenMS::Internal::MzXMLHandler::PeakType</a></div><div class="ttdeci">MapType::PeakType PeakType</div><div class="ttdoc">Peak type. </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:162</div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_a6440df7f4dbfc4c3370e2b6781bc74e5a27028cc8b5d6f0a1cb3030c180019abc"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#a6440df7f4dbfc4c3370e2b6781bc74e5a27028cc8b5d6f0a1cb3030c180019abc">OpenMS::SourceFile::SHA1</a></div><div class="ttdoc">Secure Hash Algorithm-1. </div><div class="ttdef"><b>Definition:</b> SourceFile.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html_a9d7de80efbcfc8f49025772de7806a23"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html#a9d7de80efbcfc8f49025772de7806a23">OpenMS::ContactPerson::getURL</a></div><div class="ttdeci">const String & getURL() const </div><div class="ttdoc">returns the email address </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a5a6d515dafa7fe4da638001e91bf1767"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5a6d515dafa7fe4da638001e91bf1767">OpenMS::Internal::MzXMLHandler::s_last_</a></div><div class="ttdeci">static const XMLCh * s_last_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:240</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0af3d1715feea7314cc0ed1080191ea57d"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0af3d1715feea7314cc0ed1080191ea57d">OpenMS::InstrumentSettings::CRM</a></div><div class="ttdoc">Consecutive reaction monitoring scan Synonyms: &#39;CRM scan&#39;. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html_ac02fa25060dabd021d726903e7d0d2ea"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html#ac02fa25060dabd021d726903e7d0d2ea">OpenMS::ContactPerson::getFirstName</a></div><div class="ttdeci">const String & getFirstName() const </div><div class="ttdoc">returns the first name of the person </div></div>
<div class="ttc" id="classOpenMS_1_1Software_html_ae6b3b4b6857bc1987282e2f29611dd41"><div class="ttname"><a href="classOpenMS_1_1Software.html#ae6b3b4b6857bc1987282e2f29611dd41">OpenMS::Software::getVersion</a></div><div class="ttdeci">const String & getVersion() const </div><div class="ttdoc">returns the software version </div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_a3bbd5b209e18f9afd4d8b4308787a538"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#a3bbd5b209e18f9afd4d8b4308787a538">OpenMS::DataProcessing::getCompletionTime</a></div><div class="ttdeci">const DateTime & getCompletionTime() const </div><div class="ttdoc">returns the time of completition of the processing </div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_a8f7be6e80ef1c4599af3aa096c7f7089"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#a8f7be6e80ef1c4599af3aa096c7f7089">OpenMS::InstrumentSettings::getPolarity</a></div><div class="ttdeci">IonSource::Polarity getPolarity() const </div><div class="ttdoc">returns the polarity </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a49a0a656327c327bd73a9eac5d4b2698"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a49a0a656327c327bd73a9eac5d4b2698">OpenMS::Internal::MzXMLHandler::MzXMLHandler</a></div><div class="ttdeci">MzXMLHandler(const MapType &exp, const String &filename, const String &version, const ProgressLogger &logger)</div><div class="ttdoc">Constructor for a write-only handler. </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:82</div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a066042ae14211da37d4fa66d466bfa3e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a066042ae14211da37d4fa66d466bfa3e">OpenMS::Internal::MzXMLHandler::SpectrumType</a></div><div class="ttdeci">MSSpectrum< PeakType > SpectrumType</div><div class="ttdoc">Spectrum type. </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:164</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a6ce26a62afab55d7606ad4e92428b30c"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a6ce26a62afab55d7606ad4e92428b30c">OpenMS::InstrumentSettings::UNKNOWN</a></div><div class="ttdoc">Unknown scan method. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a3b68228d65702a6a614e8e4226d25b8d"><div class="ttname"><a href="classOpenMS_1_1String.html#a3b68228d65702a6a614e8e4226d25b8d">OpenMS::String::prefix</a></div><div class="ttdeci">String prefix(SizeType length) const </div><div class="ttdoc">returns the prefix of length length </div></div>
<div class="ttc" id="classOpenMS_1_1SourceFile_html_a5469cd06bde314b8524d14cd76df2cd1"><div class="ttname"><a href="classOpenMS_1_1SourceFile.html#a5469cd06bde314b8524d14cd76df2cd1">OpenMS::SourceFile::getChecksum</a></div><div class="ttdeci">const String & getChecksum() const </div><div class="ttdoc">returns the file&#39;s checksum </div></div>
<div class="ttc" id="classOpenMS_1_1DateTime_html"><div class="ttname"><a href="classOpenMS_1_1DateTime.html">OpenMS::DateTime</a></div><div class="ttdoc">DateTime Class. </div><div class="ttdef"><b>Definition:</b> DateTime.h:55</div></div>
<div class="ttc" id="classOpenMS_1_1ProgressLogger_html"><div class="ttname"><a href="classOpenMS_1_1ProgressLogger.html">OpenMS::ProgressLogger</a></div><div class="ttdoc">Base class for all classes that want to report their progess. </div><div class="ttdef"><b>Definition:</b> ProgressLogger.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a226b41d565aa586bd45aa7d046608511"><div class="ttname"><a href="classOpenMS_1_1String.html#a226b41d565aa586bd45aa7d046608511">OpenMS::String::substr</a></div><div class="ttdeci">String substr(size_t pos=0, size_t n=npos) const </div><div class="ttdoc">Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a81dc4d91ca22493e81272673e507a8c4"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a81dc4d91ca22493e81272673e507a8c4">OpenMS::Internal::MzXMLHandler::skip_spectrum_</a></div><div class="ttdeci">bool skip_spectrum_</div><div class="ttdoc">Flag that indicates whether this spectrum should be skipped (due to options) </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:186</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_afe58ce4b50d9287e52a90ef33e65d9d2"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#afe58ce4b50d9287e52a90ef33e65d9d2">OpenMS::SpectrumSettings::getInstrumentSettings</a></div><div class="ttdeci">const InstrumentSettings & getInstrumentSettings() const </div><div class="ttdoc">returns a const reference to the instrument settings of the current spectrum </div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9a181a4b8e81bcfae30e38dc548a5586f3"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9a181a4b8e81bcfae30e38dc548a5586f3">OpenMS::DataProcessing::PEAK_PICKING</a></div><div class="ttdoc">Peak picking (conversion from raw to peak data) </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:67</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a4ea3b391bd19b4cd96229423d1a1cf35"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4ea3b391bd19b4cd96229423d1a1cf35">OpenMS::Internal::MzXMLHandler::s_startmz_</a></div><div class="ttdeci">static const XMLCh * s_startmz_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:237</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a9e8f070ec9479603961d8ad3bf49a9a3"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a9e8f070ec9479603961d8ad3bf49a9a3">OpenMS::Internal::MzXMLHandler::decoder_</a></div><div class="ttdeci">Base64 decoder_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:178</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a109ace998423bdd876eab260df9303a2"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a109ace998423bdd876eab260df9303a2">OpenMS::Internal::MzXMLHandler::s_type_</a></div><div class="ttdeci">static const XMLCh * s_type_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:218</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9e3bb003dab9b2cf00854a1eb3b01f0a16e91cdeda492f0745dc99784570f080">OpenMS::InstrumentSettings::MASSSPECTRUM</a></div><div class="ttdoc">general spectrum type </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:56</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a3da529bd3240fa0d7148484bbef0b9d7"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a3da529bd3240fa0d7148484bbef0b9d7">OpenMS::MSSpectrum::getRT</a></div><div class="ttdeci">DoubleReal getRT() const </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:215</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_a90b48146f536d2ab932723af63f0cb15"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#a90b48146f536d2ab932723af63f0cb15">OpenMS::SpectrumSettings::getPrecursors</a></div><div class="ttdeci">const std::vector< Precursor > & getPrecursors() const </div><div class="ttdoc">returns a const reference to the precursors </div></div>
<div class="ttc" id="classOpenMS_1_1PeakFileOptions_html"><div class="ttname"><a href="classOpenMS_1_1PeakFileOptions.html">OpenMS::PeakFileOptions</a></div><div class="ttdoc">Options for loading files containing peak data. </div><div class="ttdef"><b>Definition:</b> PeakFileOptions.h:47</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1XMLHandler_html_a6476bfc5285236c19e7f731e43d05cdd"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1XMLHandler.html#a6476bfc5285236c19e7f731e43d05cdd">OpenMS::Internal::XMLHandler::cv_terms_</a></div><div class="ttdeci">std::vector< std::vector< String > > cv_terms_</div><div class="ttdoc">Array of CV term lists (one sublist denotes one term and it&#39;s children) </div><div class="ttdef"><b>Definition:</b> XMLHandler.h:192</div></div>
<div class="ttc" id="classOpenMS_1_1MassAnalyzer_html_a134230547dd6de10b20f6904d9422ec3"><div class="ttname"><a href="classOpenMS_1_1MassAnalyzer.html#a134230547dd6de10b20f6904d9422ec3">OpenMS::MassAnalyzer::AnalyzerType</a></div><div class="ttdeci">AnalyzerType</div><div class="ttdoc">analyzer type </div><div class="ttdef"><b>Definition:</b> MassAnalyzer.h:53</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a8df65a3d6767516b62d0e4c84a14a4f4"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a8df65a3d6767516b62d0e4c84a14a4f4">OpenMS::Internal::MzXMLHandler::endElement</a></div><div class="ttdeci">virtual void endElement(const XMLCh *const uri, const XMLCh *const local_name, const XMLCh *const qname)</div><div class="ttdoc">Parsing method for closing tags. </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:740</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a4e6e1cb4f8a8a0c70887c3568b86348e"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a4e6e1cb4f8a8a0c70887c3568b86348e">OpenMS::Internal::MzXMLHandler::logger_</a></div><div class="ttdeci">const ProgressLogger & logger_</div><div class="ttdoc">Progress logging class. </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:192</div></div>
<div class="ttc" id="classOpenMS_1_1InstrumentSettings_html_af9ecf94ffd05a020cce7a2d10794a192"><div class="ttname"><a href="classOpenMS_1_1InstrumentSettings.html#af9ecf94ffd05a020cce7a2d10794a192">OpenMS::InstrumentSettings::NamesOfScanMode</a></div><div class="ttdeci">static const std::string NamesOfScanMode[SIZE_OF_SCANMODE]</div><div class="ttdoc">Names of scan modes. </div><div class="ttdef"><b>Definition:</b> InstrumentSettings.h:74</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumSettings_html_ad368341c22d3447e324134c47adff081"><div class="ttname"><a href="classOpenMS_1_1SpectrumSettings.html#ad368341c22d3447e324134c47adff081">OpenMS::SpectrumSettings::getNativeID</a></div><div class="ttdeci">const String & getNativeID() const </div><div class="ttdoc">returns the native identifier for the spectrum, used by the acquisition software. ...</div></div>
<div class="ttc" id="classOpenMS_1_1MetaInfoInterface_html_acabf8a0e3c40224df62b282a5ce0318f"><div class="ttname"><a href="classOpenMS_1_1MetaInfoInterface.html#acabf8a0e3c40224df62b282a5ce0318f">OpenMS::MetaInfoInterface::metaValueExists</a></div><div class="ttdeci">bool metaValueExists(const String &name) const </div><div class="ttdoc">returns if this MetaInfo is set </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a5212e012d8c0950cb3070648f396f31a"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a5212e012d8c0950cb3070648f396f31a">OpenMS::Internal::MzXMLHandler::s_filename_</a></div><div class="ttdeci">static const XMLCh * s_filename_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:221</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a742bdba7e6348fe6c549aada2a116944"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a742bdba7e6348fe6c549aada2a116944">OpenMS::Internal::MzXMLHandler::characters</a></div><div class="ttdeci">virtual void characters(const XMLCh *const chars, const XMLSize_t length)</div><div class="ttdoc">Parsing method for character data. </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:826</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_a305141aabee4495bc55a45971af1f05e"><div class="ttname"><a href="classOpenMS_1_1String.html#a305141aabee4495bc55a45971af1f05e">OpenMS::String::suffix</a></div><div class="ttdeci">String suffix(SizeType length) const </div><div class="ttdoc">returns the suffix of length length </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a037915e92e9c138bbb22b3525420ad63"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a037915e92e9c138bbb22b3525420ad63">OpenMS::Internal::MzXMLHandler::initStaticMembers_</a></div><div class="ttdeci">void initStaticMembers_()</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:251</div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html_a36df0ae8f5b0e98a1e0009ccbf8e1972"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html#a36df0ae8f5b0e98a1e0009ccbf8e1972">OpenMS::ContactPerson::getLastName</a></div><div class="ttdeci">const String & getLastName() const </div><div class="ttdoc">returns the last name of the person </div></div>
<div class="ttc" id="group__Concept_html_ga7cc214a236ad3bb6ad435bdcf5262a3f"><div class="ttname"><a href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">OpenMS::Int</a></div><div class="ttdeci">int Int</div><div class="ttdoc">Signed integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:100</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a21e306967405afb217201901a2d75351"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a21e306967405afb217201901a2d75351">OpenMS::Internal::MzXMLHandler::exp_</a></div><div class="ttdeci">MapType * exp_</div><div class="ttdoc">map pointer for reading </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:169</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_ad4338125b7a3027c186a41d554d63a74"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ad4338125b7a3027c186a41d554d63a74">OpenMS::Internal::MzXMLHandler::s_endmz_</a></div><div class="ttdeci">static const XMLCh * s_endmz_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:238</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_ac0db93030014443d6a620ac7459c1814"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#ac0db93030014443d6a620ac7459c1814">OpenMS::Internal::MzXMLHandler::s_deisotoped_</a></div><div class="ttdeci">static const XMLCh * s_deisotoped_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:247</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_ae580d960e12c7f0ebc5c95931cf39ad5"><div class="ttname"><a href="classOpenMS_1_1String.html#ae580d960e12c7f0ebc5c95931cf39ad5">OpenMS::String::split</a></div><div class="ttdeci">bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const </div><div class="ttdoc">Splits a string into substrings using splitter as delimiter. </div></div>
<div class="ttc" id="classOpenMS_1_1ContactPerson_html_aa40d949517afa236a88a9eb41ea4f35c"><div class="ttname"><a href="classOpenMS_1_1ContactPerson.html#aa40d949517afa236a88a9eb41ea4f35c">OpenMS::ContactPerson::getEmail</a></div><div class="ttdeci">const String & getEmail() const </div><div class="ttdoc">returns the email address </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a35ef4771d9814aae9cf44ba7feda927a"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a35ef4771d9814aae9cf44ba7feda927a">OpenMS::Internal::MzXMLHandler::s_uri_</a></div><div class="ttdeci">static const XMLCh * s_uri_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:243</div></div>
<div class="ttc" id="XMLHandler_8h_html"><div class="ttname"><a href="XMLHandler_8h.html">XMLHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1DataProcessing_html_af8d7ce8405ff2af127df2f9a1234f3b9ad6aaf5187119b5738f4648dcb932c240"><div class="ttname"><a href="classOpenMS_1_1DataProcessing.html#af8d7ce8405ff2af127df2f9a1234f3b9ad6aaf5187119b5738f4648dcb932c240">OpenMS::DataProcessing::CHARGE_DECONVOLUTION</a></div><div class="ttdoc">Charge deconvolution. </div><div class="ttdef"><b>Definition:</b> DataProcessing.h:61</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a265fc94e4af4dab38234d47a0132342b"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a265fc94e4af4dab38234d47a0132342b">OpenMS::Internal::MzXMLHandler::MzXMLHandler</a></div><div class="ttdeci">MzXMLHandler()</div><div class="ttdoc">Not implemented. </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a0038ff865ac073e00ca829d977f2ccdf"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a0038ff865ac073e00ca829d977f2ccdf">OpenMS::Internal::MzXMLHandler::writeTo</a></div><div class="ttdeci">void writeTo(std::ostream &os)</div><div class="ttdoc">Write the contents to a stream. </div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:885</div></div>
<div class="ttc" id="Base64_8h_html"><div class="ttname"><a href="Base64_8h.html">Base64.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Precursor_html_ac6f71e641c709dfabecce317d07ac4f7"><div class="ttname"><a href="classOpenMS_1_1Precursor.html#ac6f71e641c709dfabecce317d07ac4f7">OpenMS::Precursor::getIsolationWindowLowerOffset</a></div><div class="ttdeci">DoubleReal getIsolationWindowLowerOffset() const </div><div class="ttdoc">returns the lower offset from the target m/z </div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a65a51a09b69d61cd87bf7a27277e3aee"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a65a51a09b69d61cd87bf7a27277e3aee">OpenMS::Internal::MzXMLHandler::s_filetype_</a></div><div class="ttdeci">static const XMLCh * s_filetype_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:222</div></div>
<div class="ttc" id="String_8h_html"><div class="ttname"><a href="String_8h.html">String.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a38c21cb338ee0526513fdd9f8b701a59"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a38c21cb338ee0526513fdd9f8b701a59">OpenMS::Internal::MzXMLHandler::s_intensitycutoff_</a></div><div class="ttdeci">static const XMLCh * s_intensitycutoff_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:245</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a0a4ccd2c235c704e0ade926b45f43302"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a0a4ccd2c235c704e0ade926b45f43302">OpenMS::Internal::MzXMLHandler::s_mslevel_</a></div><div class="ttdeci">static const XMLCh * s_mslevel_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:232</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a8554c50fb31c748b177745c43a06c595"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a8554c50fb31c748b177745c43a06c595">OpenMS::Internal::MzXMLHandler::s_email_</a></div><div class="ttdeci">static const XMLCh * s_email_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:242</div></div>
<div class="ttc" id="classOpenMS_1_1IonSource_html_a84a045fa4024e050ca8be6d33311a054"><div class="ttname"><a href="classOpenMS_1_1IonSource.html#a84a045fa4024e050ca8be6d33311a054">OpenMS::IonSource::Polarity</a></div><div class="ttdeci">Polarity</div><div class="ttdoc">Polarity of the ion source. </div><div class="ttdef"><b>Definition:</b> IonSource.h:140</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_aa28e3da88956cfad247756b999df9abb"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aa28e3da88956cfad247756b999df9abb">OpenMS::Internal::MzXMLHandler::s_precursorintensity_</a></div><div class="ttdeci">static const XMLCh * s_precursorintensity_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:229</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a802a9eebc4a92192e11cd7aabec3d204"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a802a9eebc4a92192e11cd7aabec3d204">OpenMS::Internal::MzXMLHandler::s_compressionType_</a></div><div class="ttdeci">static const XMLCh * s_compressionType_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:228</div></div>
<div class="ttc" id="classOpenMS_1_1String_html_ae1870a969417d19a33f225046a66a58d"><div class="ttname"><a href="classOpenMS_1_1String.html#ae1870a969417d19a33f225046a66a58d">OpenMS::String::hasPrefix</a></div><div class="ttdeci">bool hasPrefix(const String &string) const </div><div class="ttdoc">true if String begins with string, false otherwise </div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1ParseError_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1ParseError.html">OpenMS::Exception::ParseError</a></div><div class="ttdoc">Parse Error exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:608</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_aafa58529452e61b34695d15a8fc44bc2"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#aafa58529452e61b34695d15a8fc44bc2">OpenMS::Internal::MzXMLHandler::s_windowwideness_</a></div><div class="ttdeci">static const XMLCh * s_windowwideness_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:231</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_adedd602ddb223d01302622fd5f5d3d5f"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#adedd602ddb223d01302622fd5f5d3d5f">OpenMS::Internal::MzXMLHandler::s_chargedeconvoluted_</a></div><div class="ttdeci">static const XMLCh * s_chargedeconvoluted_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:248</div></div>
<div class="ttc" id="classOpenMS_1_1Internal_1_1MzXMLHandler_html_a390ecbd61eb171e0a00bff4616452d25"><div class="ttname"><a href="classOpenMS_1_1Internal_1_1MzXMLHandler.html#a390ecbd61eb171e0a00bff4616452d25">OpenMS::Internal::MzXMLHandler::s_precision_</a></div><div class="ttdeci">static const XMLCh * s_precision_</div><div class="ttdef"><b>Definition:</b> MzXMLHandler.h:225</div></div>
</div><!-- fragment --></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 11:19:18 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>
|
