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
|
<HTML>
<HEAD>
<TITLE>TwoDOptimization.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_9f700962877a340cb515a8f4e78fa50c.html">TRANSFORMATIONS</a></li><li class="navelem"><a class="el" href="dir_29b0625679bb708bf770027bc72bc5d8.html">RAW2PEAK</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="headertitle">
<div class="title">TwoDOptimization.h</div> </div>
</div><!--header-->
<div class="contents">
<a href="TwoDOptimization_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: Alexandra Zerck $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: $</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_TRANSFORMATIONS_RAW2PEAK_TWODOPTIMIZATION_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_TRANSFORMATIONS_RAW2PEAK_TWODOPTIMIZATION_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="comment">//#define DEBUG_2D</span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#undef DEBUG_2D</span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="preprocessor"></span><span class="preprocessor">#include <iostream></span></div>
<div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <fstream></span></div>
<div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <vector></span></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span> <span class="preprocessor">#include <utility></span></div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="preprocessor">#include <cmath></span></div>
<div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#include <set></span></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="preprocessor">#include <<a class="code" href="PeakShape_8h.html">OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakShape.h</a>></span></div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="preprocessor">#include <<a class="code" href="OptimizePeakDeconvolution_8h.html">OpenMS/TRANSFORMATIONS/RAW2PEAK/OptimizePeakDeconvolution.h</a>></span></div>
<div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor">#include <<a class="code" href="MSExperiment_8h.html">OpenMS/KERNEL/MSExperiment.h</a>></span></div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span> <span class="preprocessor">#include <<a class="code" href="MSSpectrum_8h.html">OpenMS/KERNEL/MSSpectrum.h</a>></span></div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <span class="preprocessor">#include <<a class="code" href="PeakIndex_8h.html">OpenMS/KERNEL/PeakIndex.h</a>></span></div>
<div class="line"><a name="l00056"></a><span class="lineno"> 56</span> <span class="preprocessor">#include <<a class="code" href="Exception_8h.html">OpenMS/CONCEPT/Exception.h</a>></span></div>
<div class="line"><a name="l00057"></a><span class="lineno"> 57</span> <span class="preprocessor">#include <<a class="code" href="IsotopeCluster_8h.html">OpenMS/DATASTRUCTURES/IsotopeCluster.h</a>></span></div>
<div class="line"><a name="l00058"></a><span class="lineno"> 58</span> <span class="preprocessor">#include <<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>></span></div>
<div class="line"><a name="l00059"></a><span class="lineno"> 59</span> </div>
<div class="line"><a name="l00060"></a><span class="lineno"> 60</span> <span class="preprocessor">#ifndef OPENMS_SYSTEM_STOPWATCH_H</span></div>
<div class="line"><a name="l00061"></a><span class="lineno"> 61</span> <span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00062"></a><span class="lineno"> 62</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00063"></a><span class="lineno"> 63</span> <span class="preprocessor">#include <boost/math/special_functions/acosh.hpp></span></div>
<div class="line"><a name="l00064"></a><span class="lineno"> 64</span> <span class="preprocessor">#include <gsl/gsl_vector.h></span></div>
<div class="line"><a name="l00065"></a><span class="lineno"> 65</span> <span class="preprocessor">#include <gsl/gsl_multifit_nlin.h></span></div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span> <span class="preprocessor">#include <gsl/gsl_blas.h></span></div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> <span class="preprocessor">#include <<a class="code" href="OptimizePick_8h.html">OpenMS/TRANSFORMATIONS/RAW2PEAK/OptimizePick.h</a>></span></div>
<div class="line"><a name="l00068"></a><span class="lineno"> 68</span> <span class="preprocessor">#include <<a class="code" href="PeakShape_8h.html">OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakShape.h</a>></span></div>
<div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div>
<div class="line"><a name="l00070"></a><span class="lineno"> 70</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00071"></a><span class="lineno"> 71</span> {</div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html"> 86</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a> :</div>
<div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00088"></a><span class="lineno"> 88</span>  {</div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span> </div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a>();</div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> </div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a>& opt);</div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> </div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#ae71d03ba24d6ab714f95b65a524b9ec4"> 98</a></span>  <span class="keyword">virtual</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#ae71d03ba24d6ab714f95b65a524b9ec4">~TwoDOptimization</a>(){}</div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> </div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a>& operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a>& opt);</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> </div>
<div class="line"><a name="l00105"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#aafe5d0ee09d7e6ee8a5f12b9f5f40a19"> 105</a></span>  <span class="keyword">inline</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#aafe5d0ee09d7e6ee8a5f12b9f5f40a19">getMZTolerance</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> tolerance_mz_; }</div>
<div class="line"><a name="l00107"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#aef02420ae0f171972e40c069ec5931be"> 107</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#aef02420ae0f171972e40c069ec5931be">setMZTolerance</a>(<a class="code" href="classdouble.html">DoubleReal</a> tolerance_mz)</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>  tolerance_mz_ = tolerance_mz;</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span>  param_.setValue(<span class="stringliteral">"2d:tolerance_mz"</span>, tolerance_mz);</div>
<div class="line"><a name="l00111"></a><span class="lineno"> 111</span>  }</div>
<div class="line"><a name="l00112"></a><span class="lineno"> 112</span> </div>
<div class="line"><a name="l00114"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#add19caffdc34d20e18e084922846ec3a"> 114</a></span>  <span class="keyword">inline</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#add19caffdc34d20e18e084922846ec3a">getMaxPeakDistance</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> max_peak_distance_; }</div>
<div class="line"><a name="l00116"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#afe966e2a453a2c21000f38f431bc6205"> 116</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#afe966e2a453a2c21000f38f431bc6205">setMaxPeakDistance</a>(<a class="code" href="classdouble.html">DoubleReal</a> max_peak_distance)</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>  max_peak_distance_ = max_peak_distance;</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  param_.setValue(<span class="stringliteral">"2d:max_peak_distance"</span>, max_peak_distance);</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> </div>
<div class="line"><a name="l00123"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a8e66c4bb9601b0c87307512a044930b8"> 123</a></span>  <span class="keyword">inline</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a8e66c4bb9601b0c87307512a044930b8">getMaxAbsError</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> eps_abs_; }</div>
<div class="line"><a name="l00125"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a850156405bdec2d3a4761d49310151e7"> 125</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a850156405bdec2d3a4761d49310151e7">setMaxAbsError</a>(<a class="code" href="classdouble.html">DoubleReal</a> eps_abs)</div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  {</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  eps_abs_ = eps_abs;</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  param_.setValue(<span class="stringliteral">"delta_abs_error"</span>, eps_abs);</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  }</div>
<div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div>
<div class="line"><a name="l00132"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#ac061845432fbff0f67d3212a815ebac9"> 132</a></span>  <span class="keyword">inline</span> <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#ac061845432fbff0f67d3212a815ebac9">getMaxRelError</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> eps_rel_; }</div>
<div class="line"><a name="l00134"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a6ed5164a8b4af4b3de8e04912350acfb"> 134</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a6ed5164a8b4af4b3de8e04912350acfb">setMaxRelError</a>(<a class="code" href="classdouble.html">DoubleReal</a> eps_rel)</div>
<div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  {</div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span>  eps_rel_ = eps_rel;</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  param_.setValue(<span class="stringliteral">"delta_rel_error"</span>, eps_rel);</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  }</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div>
<div class="line"><a name="l00141"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a4c366f74747bc1983e91ca37d58af808"> 141</a></span>  <span class="keyword">inline</span> <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a4c366f74747bc1983e91ca37d58af808">getMaxIterations</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> max_iteration_; }</div>
<div class="line"><a name="l00143"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#ae11715606af5b9d6d8426dd7f6c783af"> 143</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#ae11715606af5b9d6d8426dd7f6c783af">setMaxIterations</a>(<a class="code" href="classunsigned_01int.html">UInt</a> max_iteration)</div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  {</div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  max_iteration_ = max_iteration;</div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  param_.setValue(<span class="stringliteral">"iterations"</span>, max_iteration);</div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  }</div>
<div class="line"><a name="l00148"></a><span class="lineno"> 148</span> </div>
<div class="line"><a name="l00150"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#aacb90f036a8fff25704290ac0c34364c"> 150</a></span>  <span class="keyword">inline</span> <span class="keyword">const</span> <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a>& <a class="code" href="classOpenMS_1_1TwoDOptimization.html#aacb90f036a8fff25704290ac0c34364c">getPenalties</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> penalties_; }</div>
<div class="line"><a name="l00152"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a165bfd792d0e5b693e0cdd6a9782d27f"> 152</a></span>  <span class="keyword">inline</span> <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a165bfd792d0e5b693e0cdd6a9782d27f">setPenalties</a>(<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a>& penalties)</div>
<div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  {</div>
<div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  penalties_ = penalties;</div>
<div class="line"><a name="l00155"></a><span class="lineno"> 155</span>  param_.setValue(<span class="stringliteral">"penalties:position"</span>, penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a5e9dd75fc35bca3ebe4981821077aebe">pos</a>);</div>
<div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  param_.setValue(<span class="stringliteral">"penalties:height"</span>, penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html#a5343d7f469d61e6d3f4808a609094175">height</a>);</div>
<div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  param_.setValue(<span class="stringliteral">"penalties:left_width"</span>, penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#abb10592f0ea83f824c0a14f4afa95be4">lWidth</a>);</div>
<div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  param_.setValue(<span class="stringliteral">"penalties:right_width"</span>, penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a478a632c0b5a363e215061428eee1a1c">rWidth</a>);</div>
<div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  }</div>
<div class="line"><a name="l00160"></a><span class="lineno"> 160</span> </div>
<div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputSpectrumIterator, <span class="keyword">typename</span> OutputPeakType></div>
<div class="line"><a name="l00178"></a><span class="lineno"> 178</span>  <span class="keywordtype">void</span> optimize(InputSpectrumIterator first,</div>
<div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  InputSpectrumIterator last,</div>
<div class="line"><a name="l00180"></a><span class="lineno"> 180</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<OutputPeakType></a>& ms_exp, <span class="keywordtype">bool</span> real2D = <span class="keyword">true</span>);</div>
<div class="line"><a name="l00181"></a><span class="lineno"> 181</span> </div>
<div class="line"><a name="l00182"></a><span class="lineno"> 182</span> </div>
<div class="line"><a name="l00183"></a><span class="lineno"> 183</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00185"></a><span class="lineno"><a class="line" href="structOpenMS_1_1TwoDOptimization_1_1Data.html"> 185</a></span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html">Data</a></div>
<div class="line"><a name="l00186"></a><span class="lineno"> 186</span>  {</div>
<div class="line"><a name="l00187"></a><span class="lineno"><a class="line" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c"> 187</a></span>  std::vector<std::pair<SignedSize, SignedSize> > <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>;</div>
<div class="line"><a name="l00188"></a><span class="lineno"><a class="line" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638"> 188</a></span>  std::multimap<DoubleReal, IsotopeCluster>::iterator <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">iso_map_iter</a>;</div>
<div class="line"><a name="l00189"></a><span class="lineno"><a class="line" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a9d5caa74a619fd37c7352fce078259fd"> 189</a></span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a9d5caa74a619fd37c7352fce078259fd">total_nr_peaks</a>;</div>
<div class="line"><a name="l00190"></a><span class="lineno"><a class="line" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a1e60993834d6cab4067738dfd729dad0"> 190</a></span>  std::map<Int, std::vector<PeakIndex> > <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a1e60993834d6cab4067738dfd729dad0">matching_peaks</a>;</div>
<div class="line"><a name="l00191"></a><span class="lineno"><a class="line" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a2dcab4dd664c2b08f478ebde32edaa74"> 191</a></span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<></a> <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a2dcab4dd664c2b08f478ebde32edaa74">picked_peaks</a>;</div>
<div class="line"><a name="l00192"></a><span class="lineno"><a class="line" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a16930394d61d06ff8227219211874592"> 192</a></span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<Peak1D>::ConstIterator</a> <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a16930394d61d06ff8227219211874592">raw_data_first</a>;</div>
<div class="line"><a name="l00193"></a><span class="lineno"><a class="line" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a4dbfc949c1c63f8a02dafd6a592d7955"> 193</a></span>  <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a> <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a4dbfc949c1c63f8a02dafd6a592d7955">penalties</a>;</div>
<div class="line"><a name="l00194"></a><span class="lineno"><a class="line" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a5e129442f31432fc1dbb5d3573754012"> 194</a></span>  std::vector<DoubleReal> <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a5e129442f31432fc1dbb5d3573754012">positions</a>;</div>
<div class="line"><a name="l00195"></a><span class="lineno"><a class="line" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a34171d03bcd36d5482f4c90b6e7c0d45"> 195</a></span>  std::vector<DoubleReal> <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a34171d03bcd36d5482f4c90b6e7c0d45">signal</a>;</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> </div>
<div class="line"><a name="l00199"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0"> 199</a></span>  std::multimap<DoubleReal, IsotopeCluster> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a>;</div>
<div class="line"><a name="l00200"></a><span class="lineno"> 200</span> </div>
<div class="line"><a name="l00202"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#af0c0642cd0366fd192034cf58036fb11"> 202</a></span>  std::multimap<DoubleReal, IsotopeCluster>::const_iterator <a class="code" href="classOpenMS_1_1TwoDOptimization.html#af0c0642cd0366fd192034cf58036fb11">curr_region_</a>;</div>
<div class="line"><a name="l00203"></a><span class="lineno"> 203</span> </div>
<div class="line"><a name="l00205"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a58b5225db8586aea7dd011a7447de6af"> 205</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a58b5225db8586aea7dd011a7447de6af">max_peak_distance_</a>;</div>
<div class="line"><a name="l00206"></a><span class="lineno"> 206</span> </div>
<div class="line"><a name="l00208"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#acbc4c0b42c88614c321ed3a8e4075c08"> 208</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#acbc4c0b42c88614c321ed3a8e4075c08">tolerance_mz_</a>;</div>
<div class="line"><a name="l00209"></a><span class="lineno"> 209</span> </div>
<div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  <span class="comment">// std::map<Int, std::vector<MSExperiment<>::SpectrumType::Iterator > > matching_peaks_;</span></div>
<div class="line"><a name="l00212"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a50d07207174c609658e117b2aa89cb10"> 212</a></span>  std::map<Int, std::vector<PeakIndex> > <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a50d07207174c609658e117b2aa89cb10">matching_peaks_</a>;</div>
<div class="line"><a name="l00213"></a><span class="lineno"> 213</span> </div>
<div class="line"><a name="l00214"></a><span class="lineno"> 214</span> </div>
<div class="line"><a name="l00216"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a1ba9944277216253f5225aa74581147e"> 216</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a1ba9944277216253f5225aa74581147e">eps_abs_</a>;</div>
<div class="line"><a name="l00217"></a><span class="lineno"> 217</span> </div>
<div class="line"><a name="l00219"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a0409337ea8ad2ae8fde8f6cba1e889a2"> 219</a></span>  <a class="code" href="classdouble.html">DoubleReal</a> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0409337ea8ad2ae8fde8f6cba1e889a2">eps_rel_</a>;</div>
<div class="line"><a name="l00220"></a><span class="lineno"> 220</span> </div>
<div class="line"><a name="l00222"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a78c0d505b8706df48e8cf696e21035ee"> 222</a></span>  <a class="code" href="classunsigned_01int.html">UInt</a> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a78c0d505b8706df48e8cf696e21035ee">max_iteration_</a>;</div>
<div class="line"><a name="l00223"></a><span class="lineno"> 223</span> </div>
<div class="line"><a name="l00225"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a5ecbb7085dd05993affbe76a8eae8718"> 225</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a5ecbb7085dd05993affbe76a8eae8718">real_2D_</a>;</div>
<div class="line"><a name="l00226"></a><span class="lineno"> 226</span> </div>
<div class="line"><a name="l00227"></a><span class="lineno"> 227</span> </div>
<div class="line"><a name="l00229"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a1491750eda19a5fae8d6aa0deafb60ce"> 229</a></span>  <a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a1491750eda19a5fae8d6aa0deafb60ce">penalties_</a>;</div>
<div class="line"><a name="l00230"></a><span class="lineno"> 230</span> </div>
<div class="line"><a name="l00231"></a><span class="lineno"> 231</span> </div>
<div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  <span class="keyword">static</span> <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> residual2D_(<span class="keyword">const</span> gsl_vector* x, <span class="keywordtype">void</span>* params, gsl_vector* f);</div>
<div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="keyword">static</span> <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> jacobian2D_(<span class="keyword">const</span> gsl_vector* x, <span class="keywordtype">void</span>* params, gsl_matrix* J);</div>
<div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  <span class="keyword">static</span> <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> evaluate2D_(<span class="keyword">const</span> gsl_vector* x, <span class="keywordtype">void</span>* params, gsl_vector* f, gsl_matrix* J);</div>
<div class="line"><a name="l00242"></a><span class="lineno"> 242</span> </div>
<div class="line"><a name="l00243"></a><span class="lineno"> 243</span> </div>
<div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  std::vector<DoubleReal>::iterator searchInScan_(std::vector<DoubleReal>::iterator scan_begin,</div>
<div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  std::vector<DoubleReal>::iterator scan_end,</div>
<div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  <a class="code" href="classdouble.html">DoubleReal</a> current_mz);</div>
<div class="line"><a name="l00251"></a><span class="lineno"> 251</span> </div>
<div class="line"><a name="l00253"></a><span class="lineno"> 253</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputSpectrumIterator, <span class="keyword">typename</span> OutputPeakType></div>
<div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  <span class="keywordtype">void</span> optimizeRegions_(InputSpectrumIterator& first,</div>
<div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  InputSpectrumIterator& last,</div>
<div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<OutputPeakType></a>& ms_exp);</div>
<div class="line"><a name="l00257"></a><span class="lineno"> 257</span> </div>
<div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputSpectrumIterator, <span class="keyword">typename</span> OutputPeakType></div>
<div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <span class="keywordtype">void</span> optimizeRegionsScanwise_(InputSpectrumIterator& first,</div>
<div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  InputSpectrumIterator& last,</div>
<div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<OutputPeakType></a>& ms_exp);</div>
<div class="line"><a name="l00263"></a><span class="lineno"> 263</span> </div>
<div class="line"><a name="l00264"></a><span class="lineno"> 264</span> </div>
<div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputSpectrumIterator, <span class="keyword">typename</span> OutputPeakType></div>
<div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <span class="keywordtype">void</span> getRegionEndpoints_(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<OutputPeakType></a>& exp,</div>
<div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  InputSpectrumIterator& first,</div>
<div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  InputSpectrumIterator& last,</div>
<div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> iso_map_idx,</div>
<div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  <a class="code" href="classdouble.html">DoubleReal</a> noise_level,</div>
<div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html">TwoDOptimization::Data</a>& d);</div>
<div class="line"><a name="l00273"></a><span class="lineno"> 273</span> </div>
<div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  <span class="keywordtype">void</span> findMatchingPeaks_(std::multimap<DoubleReal, IsotopeCluster>::iterator& it,</div>
<div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<></a>& ms_exp);</div>
<div class="line"><a name="l00277"></a><span class="lineno"> 277</span> </div>
<div class="line"><a name="l00279"></a><span class="lineno"> 279</span> </div>
<div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="keywordtype">void</span> updateMembers_();</div>
<div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  };</div>
<div class="line"><a name="l00283"></a><span class="lineno"> 283</span> </div>
<div class="line"><a name="l00284"></a><span class="lineno"> 284</span> </div>
<div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputSpectrumIterator, <span class="keyword">typename</span> OutputPeakType></div>
<div class="line"><a name="l00286"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a5678eb60386afb7f97145b361bd3947f"> 286</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a5678eb60386afb7f97145b361bd3947f">TwoDOptimization::optimize</a>(InputSpectrumIterator first, InputSpectrumIterator last, <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<OutputPeakType></a>& ms_exp, <span class="keywordtype">bool</span> real2D)</div>
<div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  {</div>
<div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  <span class="comment">//#define DEBUG_2D</span></div>
<div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  <span class="comment">//check if the input maps have the same number of spectra</span></div>
<div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  <span class="keywordflow">if</span> ((<a class="code" href="classunsigned_01int.html">UInt</a>)distance(first, last) != ms_exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>())</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">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1IllegalArgument.html">Exception::IllegalArgument</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"Error in Two2Optimization: Raw and peak map do not have the same number of spectra"</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>  <span class="comment">//do nothing if there are no scans</span></div>
<div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  <span class="keywordflow">if</span> (ms_exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">empty</a>())</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="keywordflow">return</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">//check if required meta data arrays are present (for each scan)</span></div>
<div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < ms_exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>(); ++i)</div>
<div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  {</div>
<div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  <span class="comment">//check if enough meta data arrays are present</span></div>
<div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  <span class="keywordflow">if</span> (ms_exp[i].getFloatDataArrays().<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() < 6)</div>
<div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  {</div>
<div class="line"><a name="l00305"></a><span class="lineno"> 305</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1IllegalArgument.html">Exception::IllegalArgument</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"Error in Two2Optimization: Not enough meta data arrays present (1:area, 5:shape, 3:left width, 4:right width)"</span>);</div>
<div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  }</div>
<div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  <span class="keywordtype">bool</span> area = ms_exp[i].getFloatDataArrays()[1].getName() == <span class="stringliteral">"maximumIntensity"</span>;</div>
<div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  <span class="keywordtype">bool</span> wleft = ms_exp[i].getFloatDataArrays()[3].getName() == <span class="stringliteral">"leftWidth"</span>;</div>
<div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  <span class="keywordtype">bool</span> wright = ms_exp[i].getFloatDataArrays()[4].getName() == <span class="stringliteral">"rightWidth"</span>;</div>
<div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  <span class="keywordtype">bool</span> shape = ms_exp[i].getFloatDataArrays()[5].getName() == <span class="stringliteral">"peakShape"</span>;</div>
<div class="line"><a name="l00311"></a><span class="lineno"> 311</span> </div>
<div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="keywordflow">if</span> (!area || !wleft || !wright || !shape)</div>
<div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  {</div>
<div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1IllegalArgument.html">Exception::IllegalArgument</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">"Error in Two2Optimization: One or several meta data arrays missing (1:intensity, 5:shape, 3:left width, 4:right width)"</span>);</div>
<div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  }</div>
<div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  }</div>
<div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a5ecbb7085dd05993affbe76a8eae8718">real_2D_</a> = real2D;</div>
<div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> InputSpectrumIterator::value_type InputSpectrumType;</div>
<div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> InputSpectrumType::value_type <a class="code" href="namespaceOpenMS.html#a013338b7bdbb5c3b4c78666656070e23">PeakType</a>;</div>
<div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  <span class="keyword">typedef</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> SpectrumType;</div>
<div class="line"><a name="l00321"></a><span class="lineno"> 321</span> </div>
<div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#a3049e1d8765313f967f17885188d767c">MSExperiment<OutputPeakType>::Iterator</a> ms_exp_it = ms_exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>();</div>
<div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#a3049e1d8765313f967f17885188d767c">MSExperiment<OutputPeakType>::Iterator</a> ms_exp_it_end = ms_exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">end</a>();</div>
<div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  <span class="keywordflow">if</span> (ms_exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">empty</a>())</div>
<div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  {</div>
<div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  std::cout << <span class="stringliteral">"empty experiment"</span> << std::endl;</div>
<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  <span class="keywordflow">return</span>;</div>
<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  }</div>
<div class="line"><a name="l00329"></a><span class="lineno"> 329</span>  <span class="comment">// stores the monoisotopic peaks of isotopic clusters</span></div>
<div class="line"><a name="l00330"></a><span class="lineno"> 330</span>  std::vector<DoubleReal> iso_last_scan;</div>
<div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  std::vector<DoubleReal> iso_curr_scan;</div>
<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  std::vector<std::multimap<DoubleReal, IsotopeCluster>::iterator> clusters_last_scan;</div>
<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  std::vector<std::multimap<DoubleReal, IsotopeCluster>::iterator> clusters_curr_scan;</div>
<div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  std::multimap<DoubleReal, IsotopeCluster>::iterator cluster_iter;</div>
<div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  <a class="code" href="classdouble.html">DoubleReal</a> current_rt = ms_exp_it->getRT(), last_rt = 0;</div>
<div class="line"><a name="l00336"></a><span class="lineno"> 336</span> </div>
<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  <span class="comment">// retrieve values for accepted peaks distances</span></div>
<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a58b5225db8586aea7dd011a7447de6af">max_peak_distance_</a> = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"2d:max_peak_distance"</span>);</div>
<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  <a class="code" href="classdouble.html">DoubleReal</a> tolerance_mz = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"2d:tolerance_mz"</span>);</div>
<div class="line"><a name="l00340"></a><span class="lineno"> 340</span> </div>
<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <a class="code" href="classunsigned_01int.html">UInt</a> current_charge = 0; <span class="comment">// charge state of the current isotopic cluster</span></div>
<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  <a class="code" href="classdouble.html">DoubleReal</a> mz_in_hash = 0; <span class="comment">// used as reference to the current isotopic peak</span></div>
<div class="line"><a name="l00343"></a><span class="lineno"> 343</span> </div>
<div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  <span class="comment">// sweep through scans</span></div>
<div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> curr_scan = 0; ms_exp_it + curr_scan != ms_exp_it_end; ++curr_scan)</div>
<div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  {</div>
<div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> nr_peaks_in_scan = (ms_exp_it + curr_scan)->size();</div>
<div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  <span class="keywordflow">if</span> (nr_peaks_in_scan == 0)</div>
<div class="line"><a name="l00349"></a><span class="lineno"> 349</span>  <span class="keywordflow">continue</span>;</div>
<div class="line"><a name="l00350"></a><span class="lineno"> 350</span> </div>
<div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  <span class="comment">//last_rt = current_rt;</span></div>
<div class="line"><a name="l00352"></a><span class="lineno"> 352</span>  current_rt = (ms_exp_it + curr_scan)->getRT();</div>
<div class="line"><a name="l00353"></a><span class="lineno"> 353</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html#a6d64276a665c3c0dca8fb4ade3c8b477">MSExperiment<OutputPeakType>::SpectrumType::Iterator</a> peak_it = (ms_exp_it + curr_scan)->begin();</div>
<div class="line"><a name="l00354"></a><span class="lineno"> 354</span> </div>
<div class="line"><a name="l00355"></a><span class="lineno"> 355</span>  <span class="comment">// copy cluster information of least scan</span></div>
<div class="line"><a name="l00356"></a><span class="lineno"> 356</span>  iso_last_scan = iso_curr_scan;</div>
<div class="line"><a name="l00357"></a><span class="lineno"> 357</span>  iso_curr_scan.clear();</div>
<div class="line"><a name="l00358"></a><span class="lineno"> 358</span>  clusters_last_scan = clusters_curr_scan;</div>
<div class="line"><a name="l00359"></a><span class="lineno"> 359</span>  clusters_curr_scan.clear();</div>
<div class="line"><a name="l00360"></a><span class="lineno"> 360</span> </div>
<div class="line"><a name="l00361"></a><span class="lineno"> 361</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00362"></a><span class="lineno"> 362</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"Next scan with rt: "</span> << current_rt << std::endl;</div>
<div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  std::cout << <span class="stringliteral">"Next scan, rt = "</span> << current_rt << <span class="stringliteral">" last_rt: "</span> << last_rt << std::endl;</div>
<div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  std::cout << <span class="stringliteral">"---------------------------------------------------------------------------"</span> << std::endl;</div>
<div class="line"><a name="l00365"></a><span class="lineno"> 365</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00366"></a><span class="lineno"> 366</span> <span class="preprocessor"></span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<PeakType></a> s;</div>
<div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  s.<a class="code" href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">setRT</a>(current_rt);</div>
<div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  <span class="comment">// check if there were scans in between</span></div>
<div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  <span class="keywordflow">if</span> (last_rt == 0 || <span class="comment">// are we in the first scan</span></div>
<div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  ((lower_bound(first, last, s, <span class="keyword">typename</span> SpectrumType::RTLess()) - 1)->getRT() == last_rt))</div>
<div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  {</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> </div>
<div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  <span class="keywordflow">for</span> (<a class="code" href="classunsigned_01int.html">UInt</a> curr_peak = 0; curr_peak < (ms_exp_it + curr_scan)->size() - 1; ++curr_peak)</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> </div>
<div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  <span class="comment">// store the m/z of the current peak</span></div>
<div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  <a class="code" href="classdouble.html">DoubleReal</a> curr_mz = (peak_it + curr_peak)->getMZ();</div>
<div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  <a class="code" href="classdouble.html">DoubleReal</a> dist2nextpeak = (peak_it + curr_peak + 1)->getMZ() - curr_mz;</div>
<div class="line"><a name="l00380"></a><span class="lineno"> 380</span> </div>
<div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  <span class="keywordflow">if</span> (dist2nextpeak <= <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a58b5225db8586aea7dd011a7447de6af">max_peak_distance_</a>) <span class="comment">// one single peak without neighbors isn't optimized</span></div>
<div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  {</div>
<div class="line"><a name="l00383"></a><span class="lineno"> 383</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00384"></a><span class="lineno"> 384</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"Isotopic pattern found ! "</span> << std::endl;</div>
<div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  std::cout << <span class="stringliteral">"We are at: "</span> << (peak_it + curr_peak)->getMZ() << <span class="stringliteral">" "</span> << curr_mz << std::endl;</div>
<div class="line"><a name="l00386"></a><span class="lineno"> 386</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00387"></a><span class="lineno"> 387</span> <span class="preprocessor"></span> <span class="keywordflow">if</span> (!iso_last_scan.empty()) <span class="comment">// Did we find any isotopic cluster in the last scan?</span></div>
<div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  {</div>
<div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  std::sort(iso_last_scan.begin(), iso_last_scan.end());</div>
<div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  <span class="comment">// there were some isotopic clustures in the last scan...</span></div>
<div class="line"><a name="l00391"></a><span class="lineno"> 391</span>  std::vector<DoubleReal>::iterator it =</div>
<div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a74f373ec1e1e803064c86d9b0f18abdd">searchInScan_</a>(iso_last_scan.begin(), iso_last_scan.end(), curr_mz);</div>
<div class="line"><a name="l00393"></a><span class="lineno"> 393</span> </div>
<div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  <a class="code" href="classdouble.html">DoubleReal</a> delta_mz = fabs(*it - curr_mz);</div>
<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  <span class="comment">//std::cout << delta_mz << " "<< tolerance_mz << std::endl;</span></div>
<div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  <span class="keywordflow">if</span> (delta_mz > tolerance_mz) <span class="comment">// check if first peak of last cluster is close enough</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>  mz_in_hash = curr_mz; <span class="comment">// update current hash key</span></div>
<div class="line"><a name="l00399"></a><span class="lineno"> 399</span> </div>
<div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  <span class="comment">// create new isotopic cluster</span></div>
<div class="line"><a name="l00401"></a><span class="lineno"> 401</span> <span class="comment">// #ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00402"></a><span class="lineno"> 402</span> <span class="comment">// std::cout << "Last peak cluster too far, creating new cluster at "<<curr_mz << std::endl;</span></div>
<div class="line"><a name="l00403"></a><span class="lineno"> 403</span> <span class="comment">// #endif</span></div>
<div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  <a class="code" href="structOpenMS_1_1IsotopeCluster.html">IsotopeCluster</a> new_cluster;</div>
<div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  new_cluster.<a class="code" href="structOpenMS_1_1IsotopeCluster.html#ad4c8689a4cd1334e0eccdadcb0cc5a54">peaks</a>.<a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html#a8253a7962ca1c79b71e6af96589b7720">charge</a> = current_charge;</div>
<div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  new_cluster.<a class="code" href="structOpenMS_1_1IsotopeCluster.html#a47b3744693f84a7d94f7181676f36758">scans</a>.push_back(curr_scan);</div>
<div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  cluster_iter = <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a>.insert(std::pair<DoubleReal, IsotopeCluster>(mz_in_hash, new_cluster));</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>  }</div>
<div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  {</div>
<div class="line"><a name="l00412"></a><span class="lineno"> 412</span> <span class="comment">// //#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00413"></a><span class="lineno"> 413</span> <span class="comment">// std::cout << "Found neighbouring peak with distance (m/z) " << delta_mz << std::endl;</span></div>
<div class="line"><a name="l00414"></a><span class="lineno"> 414</span> <span class="comment">// //#endif</span></div>
<div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  cluster_iter = clusters_last_scan[distance(iso_last_scan.begin(), it)];</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="comment">// check whether this scan is already contained</span></div>
<div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  <span class="keywordflow">if</span> (find(cluster_iter->second.scans.begin(), cluster_iter->second.scans.end(), curr_scan)</div>
<div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  == cluster_iter->second.scans.end())</div>
<div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  {</div>
<div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  cluster_iter->second.scans.push_back(curr_scan);</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> </div>
<div class="line"><a name="l00424"></a><span class="lineno"> 424</span> <span class="comment">// //#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00425"></a><span class="lineno"> 425</span> <span class="comment">// std::cout << "Cluster with " << cluster_iter->second.peaks.size()</span></div>
<div class="line"><a name="l00426"></a><span class="lineno"> 426</span> <span class="comment">// << " peaks retrieved." << std::endl;</span></div>
<div class="line"><a name="l00427"></a><span class="lineno"> 427</span> <span class="comment">// //#endif</span></div>
<div class="line"><a name="l00428"></a><span class="lineno"> 428</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>  }</div>
<div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  <span class="keywordflow">else</span> <span class="comment">// last scan did not contain any isotopic cluster</span></div>
<div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  {</div>
<div class="line"><a name="l00433"></a><span class="lineno"> 433</span> <span class="comment">// //#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00434"></a><span class="lineno"> 434</span> <span class="comment">// std::cout << "Last scan was empty => creating new cluster." << std::endl;</span></div>
<div class="line"><a name="l00435"></a><span class="lineno"> 435</span> <span class="comment">// std::cout << "Creating new cluster at m/z: " << curr_mz << std::endl;</span></div>
<div class="line"><a name="l00436"></a><span class="lineno"> 436</span> <span class="comment">// //#endif</span></div>
<div class="line"><a name="l00437"></a><span class="lineno"> 437</span> </div>
<div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  mz_in_hash = curr_mz; <span class="comment">// update current hash key</span></div>
<div class="line"><a name="l00439"></a><span class="lineno"> 439</span> </div>
<div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  <span class="comment">// create new isotopic cluster</span></div>
<div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  <a class="code" href="structOpenMS_1_1IsotopeCluster.html">IsotopeCluster</a> new_cluster;</div>
<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  new_cluster.<a class="code" href="structOpenMS_1_1IsotopeCluster.html#ad4c8689a4cd1334e0eccdadcb0cc5a54">peaks</a>.<a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html#a8253a7962ca1c79b71e6af96589b7720">charge</a> = current_charge;</div>
<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  new_cluster.<a class="code" href="structOpenMS_1_1IsotopeCluster.html#a47b3744693f84a7d94f7181676f36758">scans</a>.push_back(curr_scan);</div>
<div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  cluster_iter = <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a>.insert(std::pair<DoubleReal, IsotopeCluster>(mz_in_hash, new_cluster));</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>  }</div>
<div class="line"><a name="l00447"></a><span class="lineno"> 447</span> </div>
<div class="line"><a name="l00448"></a><span class="lineno"> 448</span> <span class="comment">// //#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00449"></a><span class="lineno"> 449</span> <span class="comment">// std::cout << "Storing found peak in current isotopic cluster" << std::endl;</span></div>
<div class="line"><a name="l00450"></a><span class="lineno"> 450</span> <span class="comment">// //#endif</span></div>
<div class="line"><a name="l00451"></a><span class="lineno"> 451</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>  cluster_iter->second.peaks.insert(std::pair<UInt, UInt>(curr_scan, curr_peak));</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>  iso_curr_scan.push_back(mz_in_hash);</div>
<div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  clusters_curr_scan.push_back(cluster_iter);</div>
<div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  ++curr_peak;</div>
<div class="line"><a name="l00459"></a><span class="lineno"> 459</span> </div>
<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  cluster_iter->second.peaks.insert(std::pair<UInt, UInt>(curr_scan, curr_peak));</div>
<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  iso_curr_scan.push_back((peak_it + curr_peak)->getMZ());</div>
<div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  clusters_curr_scan.push_back(cluster_iter);</div>
<div class="line"><a name="l00463"></a><span class="lineno"> 463</span> </div>
<div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  <span class="comment">// check distance to next peak</span></div>
<div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  <span class="keywordflow">if</span> ((curr_peak + 1) >= nr_peaks_in_scan)</div>
<div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  dist2nextpeak = (peak_it + curr_peak + 1)->getMZ() - (peak_it + curr_peak)->getMZ();</div>
<div class="line"><a name="l00468"></a><span class="lineno"> 468</span> </div>
<div class="line"><a name="l00469"></a><span class="lineno"> 469</span> </div>
<div class="line"><a name="l00470"></a><span class="lineno"> 470</span>  <span class="comment">// loop until end of isotopic pattern in this scan</span></div>
<div class="line"><a name="l00471"></a><span class="lineno"> 471</span>  <span class="keywordflow">while</span> (dist2nextpeak <= <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a58b5225db8586aea7dd011a7447de6af">max_peak_distance_</a></div>
<div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  && curr_peak < (nr_peaks_in_scan - 1))</div>
<div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  {</div>
<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  cluster_iter->second.peaks.insert(std::pair<UInt, UInt>(curr_scan, curr_peak + 1)); <span class="comment">// save peak in cluster</span></div>
<div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  iso_curr_scan.push_back((peak_it + curr_peak + 1)->getMZ());</div>
<div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  clusters_curr_scan.push_back(cluster_iter);</div>
<div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  <span class="comment">// std::cout << "new enter'd: "<<(peak_it+curr_peak+1)->getMZ()<<" im while"<<std::endl;</span></div>
<div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  ++curr_peak;</div>
<div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  <span class="keywordflow">if</span> (curr_peak >= nr_peaks_in_scan - 1)</div>
<div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  dist2nextpeak = (peak_it + curr_peak + 1)->getMZ() - (peak_it + curr_peak)->getMZ(); <span class="comment">// get distance to next peak</span></div>
<div class="line"><a name="l00482"></a><span class="lineno"> 482</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="comment">// end while(...)</span></div>
<div class="line"><a name="l00485"></a><span class="lineno"> 485</span> </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> </div>
<div class="line"><a name="l00488"></a><span class="lineno"> 488</span>  } <span class="comment">// end of if (dist2nextpeak <= max_peak_distance_)</span></div>
<div class="line"><a name="l00489"></a><span class="lineno"> 489</span>  <span class="keywordflow">else</span></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>  <span class="keywordflow">if</span> (!iso_last_scan.empty()) <span class="comment">// Did we find any isotopic cluster in the last scan?</span></div>
<div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  {</div>
<div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  std::sort(iso_last_scan.begin(), iso_last_scan.end());</div>
<div class="line"><a name="l00494"></a><span class="lineno"> 494</span>  <span class="comment">// there were some isotopic clusters in the last scan...</span></div>
<div class="line"><a name="l00495"></a><span class="lineno"> 495</span>  std::vector<DoubleReal>::iterator it =</div>
<div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a74f373ec1e1e803064c86d9b0f18abdd">searchInScan_</a>(iso_last_scan.begin(), iso_last_scan.end(), curr_mz);</div>
<div class="line"><a name="l00497"></a><span class="lineno"> 497</span> </div>
<div class="line"><a name="l00498"></a><span class="lineno"> 498</span>  <a class="code" href="classdouble.html">DoubleReal</a> delta_mz = fabs(*it - curr_mz);</div>
<div class="line"><a name="l00499"></a><span class="lineno"> 499</span>  <span class="comment">// std::cout << delta_mz << " "<< tolerance_mz << std::endl;</span></div>
<div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  <span class="keywordflow">if</span> (delta_mz > tolerance_mz) <span class="comment">// check if first peak of last cluster is close enough</span></div>
<div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  {</div>
<div class="line"><a name="l00502"></a><span class="lineno"> 502</span>  mz_in_hash = curr_mz; <span class="comment">// update current hash key</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>  <span class="comment">// create new isotopic cluster</span></div>
<div class="line"><a name="l00505"></a><span class="lineno"> 505</span> <span class="comment">// //#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00506"></a><span class="lineno"> 506</span> <span class="comment">// std::cout << "Last peak cluster too far, creating new cluster at "<<curr_mz << std::endl;</span></div>
<div class="line"><a name="l00507"></a><span class="lineno"> 507</span> <span class="comment">// //#endif</span></div>
<div class="line"><a name="l00508"></a><span class="lineno"> 508</span>  <a class="code" href="structOpenMS_1_1IsotopeCluster.html">IsotopeCluster</a> new_cluster;</div>
<div class="line"><a name="l00509"></a><span class="lineno"> 509</span>  new_cluster.<a class="code" href="structOpenMS_1_1IsotopeCluster.html#ad4c8689a4cd1334e0eccdadcb0cc5a54">peaks</a>.<a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html#a8253a7962ca1c79b71e6af96589b7720">charge</a> = current_charge;</div>
<div class="line"><a name="l00510"></a><span class="lineno"> 510</span>  new_cluster.<a class="code" href="structOpenMS_1_1IsotopeCluster.html#a47b3744693f84a7d94f7181676f36758">scans</a>.push_back(curr_scan);</div>
<div class="line"><a name="l00511"></a><span class="lineno"> 511</span>  cluster_iter = <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a>.insert(std::pair<DoubleReal, IsotopeCluster>(mz_in_hash, new_cluster));</div>
<div class="line"><a name="l00512"></a><span class="lineno"> 512</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">else</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> <span class="comment">// //#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00517"></a><span class="lineno"> 517</span> <span class="comment">// std::cout << "Found neighbouring peak with distance (m/z) " << delta_mz << std::endl;</span></div>
<div class="line"><a name="l00518"></a><span class="lineno"> 518</span> <span class="comment">// //#endif</span></div>
<div class="line"><a name="l00519"></a><span class="lineno"> 519</span>  cluster_iter = clusters_last_scan[distance(iso_last_scan.begin(), it)];</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>  <span class="comment">// check whether this scan is already contained</span></div>
<div class="line"><a name="l00522"></a><span class="lineno"> 522</span>  <span class="keywordflow">if</span> (find(cluster_iter->second.scans.begin(), cluster_iter->second.scans.end(), curr_scan)</div>
<div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  == cluster_iter->second.scans.end())</div>
<div class="line"><a name="l00524"></a><span class="lineno"> 524</span>  {</div>
<div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  cluster_iter->second.scans.push_back(curr_scan);</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> </div>
<div class="line"><a name="l00528"></a><span class="lineno"> 528</span> <span class="comment">// //#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00529"></a><span class="lineno"> 529</span> <span class="comment">// std::cout << "Cluster with " << cluster_iter->second.peaks.size()</span></div>
<div class="line"><a name="l00530"></a><span class="lineno"> 530</span> <span class="comment">// << " peaks retrieved." << std::endl;</span></div>
<div class="line"><a name="l00531"></a><span class="lineno"> 531</span> <span class="comment">// //#endif</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> </div>
<div class="line"><a name="l00534"></a><span class="lineno"> 534</span>  }</div>
<div class="line"><a name="l00535"></a><span class="lineno"> 535</span>  <span class="keywordflow">else</span> <span class="comment">// last scan did not contain any isotopic cluster</span></div>
<div class="line"><a name="l00536"></a><span class="lineno"> 536</span>  {</div>
<div class="line"><a name="l00537"></a><span class="lineno"> 537</span> <span class="comment">// //#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00538"></a><span class="lineno"> 538</span> <span class="comment">// std::cout << "Last scan was empty => creating new cluster." << std::endl;</span></div>
<div class="line"><a name="l00539"></a><span class="lineno"> 539</span> <span class="comment">// std::cout << "Creating new cluster at m/z: " << curr_mz << std::endl;</span></div>
<div class="line"><a name="l00540"></a><span class="lineno"> 540</span> <span class="comment">// //#endif</span></div>
<div class="line"><a name="l00541"></a><span class="lineno"> 541</span> </div>
<div class="line"><a name="l00542"></a><span class="lineno"> 542</span>  mz_in_hash = curr_mz; <span class="comment">// update current hash key</span></div>
<div class="line"><a name="l00543"></a><span class="lineno"> 543</span> </div>
<div class="line"><a name="l00544"></a><span class="lineno"> 544</span>  <span class="comment">// create new isotopic cluster</span></div>
<div class="line"><a name="l00545"></a><span class="lineno"> 545</span>  <a class="code" href="structOpenMS_1_1IsotopeCluster.html">IsotopeCluster</a> new_cluster;</div>
<div class="line"><a name="l00546"></a><span class="lineno"> 546</span>  new_cluster.<a class="code" href="structOpenMS_1_1IsotopeCluster.html#ad4c8689a4cd1334e0eccdadcb0cc5a54">peaks</a>.<a class="code" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html#a8253a7962ca1c79b71e6af96589b7720">charge</a> = current_charge;</div>
<div class="line"><a name="l00547"></a><span class="lineno"> 547</span>  new_cluster.<a class="code" href="structOpenMS_1_1IsotopeCluster.html#a47b3744693f84a7d94f7181676f36758">scans</a>.push_back(curr_scan);</div>
<div class="line"><a name="l00548"></a><span class="lineno"> 548</span>  cluster_iter = <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a>.insert(std::pair<DoubleReal, IsotopeCluster>(mz_in_hash, new_cluster));</div>
<div class="line"><a name="l00549"></a><span class="lineno"> 549</span> </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> </div>
<div class="line"><a name="l00552"></a><span class="lineno"> 552</span> <span class="comment">// //#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00553"></a><span class="lineno"> 553</span> <span class="comment">// std::cout << "Storing found peak in current isotopic cluster" << std::endl;</span></div>
<div class="line"><a name="l00554"></a><span class="lineno"> 554</span> <span class="comment">// //#endif</span></div>
<div class="line"><a name="l00555"></a><span class="lineno"> 555</span> </div>
<div class="line"><a name="l00556"></a><span class="lineno"> 556</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>  cluster_iter->second.peaks.insert(std::pair<UInt, UInt>(curr_scan, curr_peak));</div>
<div class="line"><a name="l00559"></a><span class="lineno"> 559</span> </div>
<div class="line"><a name="l00560"></a><span class="lineno"> 560</span>  iso_curr_scan.push_back(mz_in_hash);</div>
<div class="line"><a name="l00561"></a><span class="lineno"> 561</span>  clusters_curr_scan.push_back(cluster_iter);</div>
<div class="line"><a name="l00562"></a><span class="lineno"> 562</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>  }</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>  current_charge = 0; <span class="comment">// reset charge</span></div>
<div class="line"><a name="l00567"></a><span class="lineno"> 567</span>  } <span class="comment">// end for (...)</span></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>  last_rt = current_rt;</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>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html#af0c0642cd0366fd192034cf58036fb11">curr_region_</a> = <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a>.begin();</div>
<div class="line"><a name="l00572"></a><span class="lineno"> 572</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00573"></a><span class="lineno"> 573</span> <span class="preprocessor"></span> std::cout << <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a>.size() << <span class="stringliteral">" isotopic clusters were found ! "</span> << std::endl;</div>
<div class="line"><a name="l00574"></a><span class="lineno"> 574</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00575"></a><span class="lineno"> 575</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00576"></a><span class="lineno"> 576</span>  <span class="keywordflow">if</span> (<a class="code" href="classOpenMS_1_1TwoDOptimization.html#a5ecbb7085dd05993affbe76a8eae8718">real_2D_</a>)</div>
<div class="line"><a name="l00577"></a><span class="lineno"> 577</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">optimizeRegions_</a>(first, last, ms_exp);</div>
<div class="line"><a name="l00578"></a><span class="lineno"> 578</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00579"></a><span class="lineno"> 579</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html#adca2617ab638fed2467b9d57b1fe2cfa">optimizeRegionsScanwise_</a>(first, last, ms_exp);</div>
<div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  <span class="comment">//#undef DEBUG_2D</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> </div>
<div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputSpectrumIterator, <span class="keyword">typename</span> OutputPeakType></div>
<div class="line"><a name="l00584"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba"> 584</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_</a>(InputSpectrumIterator& first,</div>
<div class="line"><a name="l00585"></a><span class="lineno"> 585</span>  InputSpectrumIterator& last,</div>
<div class="line"><a name="l00586"></a><span class="lineno"> 586</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<OutputPeakType></a>& ms_exp)</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>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> counter = 0;</div>
<div class="line"><a name="l00589"></a><span class="lineno"> 589</span>  <span class="comment">// go through the clusters</span></div>
<div class="line"><a name="l00590"></a><span class="lineno"> 590</span>  <span class="keywordflow">for</span> (std::multimap<DoubleReal, IsotopeCluster>::iterator it = <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a>.begin();</div>
<div class="line"><a name="l00591"></a><span class="lineno"> 591</span>  it != <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a>.end();</div>
<div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  ++it)</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> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00595"></a><span class="lineno"> 595</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"element: "</span> << counter << std::endl;</div>
<div class="line"><a name="l00596"></a><span class="lineno"> 596</span>  std::cout << <span class="stringliteral">"mz: "</span> << it->first << std::endl << <span class="stringliteral">"rts: "</span>;</div>
<div class="line"><a name="l00597"></a><span class="lineno"> 597</span> <span class="comment">// for(Size i=0;i<it->second.scans.size();++i) std::cout << it->second.scans[i] << "\n";</span></div>
<div class="line"><a name="l00598"></a><span class="lineno"> 598</span>  std::cout << std::endl << <span class="stringliteral">"peaks: "</span>;</div>
<div class="line"><a name="l00599"></a><span class="lineno"> 599</span>  IsotopeCluster::IndexSet::const_iterator iter = it->second.peaks.begin();</div>
<div class="line"><a name="l00600"></a><span class="lineno"> 600</span>  <span class="keywordflow">for</span> (; iter != it->second.peaks.end(); ++iter)</div>
<div class="line"><a name="l00601"></a><span class="lineno"> 601</span>  std::cout << ms_exp[iter->first].getRT() << <span class="stringliteral">" "</span> << (ms_exp[iter->first][iter->second]).getMZ() << std::endl;</div>
<div class="line"><a name="l00602"></a><span class="lineno"> 602</span> </div>
<div class="line"><a name="l00603"></a><span class="lineno"> 603</span> <span class="comment">//for(Size i=0;i<it->second.peaks.size();++i) std::cout << ms_exp[it->first].getRT() << " "<<(ms_exp[it->first][it->second]).getMZ()<<std::endl;</span></div>
<div class="line"><a name="l00604"></a><span class="lineno"> 604</span>  std::cout << std::endl << std::endl;</div>
<div class="line"><a name="l00605"></a><span class="lineno"> 605</span> </div>
<div class="line"><a name="l00606"></a><span class="lineno"> 606</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00607"></a><span class="lineno"> 607</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00608"></a><span class="lineno"> 608</span>  <span class="comment">// prepare for optimization:</span></div>
<div class="line"><a name="l00609"></a><span class="lineno"> 609</span>  <span class="comment">// determine the matching peaks</span></div>
<div class="line"><a name="l00610"></a><span class="lineno"> 610</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a50d07207174c609658e117b2aa89cb10">matching_peaks_</a>.clear();</div>
<div class="line"><a name="l00611"></a><span class="lineno"> 611</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a8e4d88640e61ef82005212a8583ba784">findMatchingPeaks_</a>(it, ms_exp);</div>
<div class="line"><a name="l00612"></a><span class="lineno"> 612</span>  <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html">TwoDOptimization::Data</a> d;</div>
<div class="line"><a name="l00613"></a><span class="lineno"> 613</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a4dbfc949c1c63f8a02dafd6a592d7955">penalties</a> = <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a1491750eda19a5fae8d6aa0deafb60ce">penalties_</a>;</div>
<div class="line"><a name="l00614"></a><span class="lineno"> 614</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a1e60993834d6cab4067738dfd729dad0">matching_peaks</a> = <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a50d07207174c609658e117b2aa89cb10">matching_peaks_</a>;</div>
<div class="line"><a name="l00615"></a><span class="lineno"> 615</span>  <span class="comment">// and the endpoints of each isotope pattern in the cluster</span></div>
<div class="line"><a name="l00616"></a><span class="lineno"> 616</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a6d2b21b20b10f65e5a6052e8c8aa84e7">getRegionEndpoints_</a>(ms_exp, first, last, counter, 400, d);</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="comment">// peaks have to be stored globally</span></div>
<div class="line"><a name="l00619"></a><span class="lineno"> 619</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">iso_map_iter</a> = it;</div>
<div class="line"><a name="l00620"></a><span class="lineno"> 620</span> </div>
<div class="line"><a name="l00621"></a><span class="lineno"> 621</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a2dcab4dd664c2b08f478ebde32edaa74">picked_peaks</a> = ms_exp;</div>
<div class="line"><a name="l00622"></a><span class="lineno"> 622</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a16930394d61d06ff8227219211874592">raw_data_first</a> = first;</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="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> nr_diff_peaks = <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a50d07207174c609658e117b2aa89cb10">matching_peaks_</a>.size();</div>
<div class="line"><a name="l00625"></a><span class="lineno"> 625</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a9d5caa74a619fd37c7352fce078259fd">total_nr_peaks</a> = it->second.peaks.size();</div>
<div class="line"><a name="l00626"></a><span class="lineno"> 626</span> </div>
<div class="line"><a name="l00627"></a><span class="lineno"> 627</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> nr_parameters = nr_diff_peaks * 3 + d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a9d5caa74a619fd37c7352fce078259fd">total_nr_peaks</a>;</div>
<div class="line"><a name="l00628"></a><span class="lineno"> 628</span> </div>
<div class="line"><a name="l00629"></a><span class="lineno"> 629</span>  gsl_vector* start_value = gsl_vector_alloc(nr_parameters);</div>
<div class="line"><a name="l00630"></a><span class="lineno"> 630</span>  gsl_vector_set_zero(start_value);</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>  <span class="comment">// initialize parameters for optimization</span></div>
<div class="line"><a name="l00633"></a><span class="lineno"> 633</span>  std::map<Int, std::vector<PeakIndex> >::iterator m_peaks_it = d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a1e60993834d6cab4067738dfd729dad0">matching_peaks</a>.begin();</div>
<div class="line"><a name="l00634"></a><span class="lineno"> 634</span>  <a class="code" href="classdouble.html">DoubleReal</a> av_mz = 0, av_lw = 0, av_rw = 0, avr_height = 0, height;</div>
<div class="line"><a name="l00635"></a><span class="lineno"> 635</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> peak_counter = 0;</div>
<div class="line"><a name="l00636"></a><span class="lineno"> 636</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> diff_peak_counter = 0;</div>
<div class="line"><a name="l00637"></a><span class="lineno"> 637</span>  <span class="comment">// go through the matching peaks</span></div>
<div class="line"><a name="l00638"></a><span class="lineno"> 638</span>  <span class="keywordflow">for</span> (; m_peaks_it != d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a1e60993834d6cab4067738dfd729dad0">matching_peaks</a>.end(); ++m_peaks_it)</div>
<div class="line"><a name="l00639"></a><span class="lineno"> 639</span>  {</div>
<div class="line"><a name="l00640"></a><span class="lineno"> 640</span>  av_mz = 0, av_lw = 0, av_rw = 0, avr_height = 0;</div>
<div class="line"><a name="l00641"></a><span class="lineno"> 641</span>  std::vector<PeakIndex>::iterator iter_iter = (m_peaks_it)->second.begin();</div>
<div class="line"><a name="l00642"></a><span class="lineno"> 642</span>  <span class="keywordflow">for</span> (; iter_iter != m_peaks_it->second.end(); ++iter_iter)</div>
<div class="line"><a name="l00643"></a><span class="lineno"> 643</span>  {</div>
<div class="line"><a name="l00644"></a><span class="lineno"> 644</span>  height = ms_exp[(iter_iter)->spectrum].getFloatDataArrays()[1][(iter_iter)->peak]; <span class="comment">//(iter_iter)->getPeak(ms_exp).getIntensity();</span></div>
<div class="line"><a name="l00645"></a><span class="lineno"> 645</span>  avr_height += height;</div>
<div class="line"><a name="l00646"></a><span class="lineno"> 646</span>  av_mz += (iter_iter)->getPeak(ms_exp).getMZ() * height;</div>
<div class="line"><a name="l00647"></a><span class="lineno"> 647</span>  av_lw += ms_exp[(iter_iter)->spectrum].getFloatDataArrays()[3][(iter_iter)->peak] * height; <span class="comment">//left width</span></div>
<div class="line"><a name="l00648"></a><span class="lineno"> 648</span>  av_rw += ms_exp[(iter_iter)->spectrum].getFloatDataArrays()[4][(iter_iter)->peak] * height; <span class="comment">//right width</span></div>
<div class="line"><a name="l00649"></a><span class="lineno"> 649</span>  gsl_vector_set(start_value, peak_counter, height);</div>
<div class="line"><a name="l00650"></a><span class="lineno"> 650</span>  ++peak_counter;</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>  gsl_vector_set(start_value, d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a9d5caa74a619fd37c7352fce078259fd">total_nr_peaks</a> + 3 * diff_peak_counter, av_mz / avr_height);</div>
<div class="line"><a name="l00653"></a><span class="lineno"> 653</span>  gsl_vector_set(start_value, d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a9d5caa74a619fd37c7352fce078259fd">total_nr_peaks</a> + 3 * diff_peak_counter + 1, av_lw / avr_height);</div>
<div class="line"><a name="l00654"></a><span class="lineno"> 654</span>  gsl_vector_set(start_value, d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a9d5caa74a619fd37c7352fce078259fd">total_nr_peaks</a> + 3 * diff_peak_counter + 2, av_rw / avr_height);</div>
<div class="line"><a name="l00655"></a><span class="lineno"> 655</span>  ++diff_peak_counter;</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> </div>
<div class="line"><a name="l00658"></a><span class="lineno"> 658</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00659"></a><span class="lineno"> 659</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"----------------------------\n\nstart_value: "</span> << std::endl;</div>
<div class="line"><a name="l00660"></a><span class="lineno"> 660</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> < start_value->size; ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</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>  std::cout << gsl_vector_get(start_value, <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>) << std::endl;</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> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00665"></a><span class="lineno"> 665</span> <span class="preprocessor"></span> <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> num_positions = 0;</div>
<div class="line"><a name="l00666"></a><span class="lineno"> 666</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>.size(); i += 2)</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>  num_positions += (d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>[i + 1].second - d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>[i].second + 1);</div>
<div class="line"><a name="l00669"></a><span class="lineno"> 669</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00670"></a><span class="lineno"> 670</span> <span class="preprocessor"></span> std::cout << d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>[i + 1].second << <span class="stringliteral">" - "</span> << d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>[i].second << <span class="stringliteral">" +1 "</span> << std::endl;</div>
<div class="line"><a name="l00671"></a><span class="lineno"> 671</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00672"></a><span class="lineno"> 672</span> <span class="preprocessor"></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> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00675"></a><span class="lineno"> 675</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"num_positions : "</span> << num_positions << std::endl;</div>
<div class="line"><a name="l00676"></a><span class="lineno"> 676</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00677"></a><span class="lineno"> 677</span> <span class="preprocessor"></span> <span class="comment">// The gsl algorithms require us to provide function pointers for the evaluation of</span></div>
<div class="line"><a name="l00678"></a><span class="lineno"> 678</span>  <span class="comment">// the target function.</span></div>
<div class="line"><a name="l00679"></a><span class="lineno"> 679</span>  gsl_multifit_function_fdf fit_function;</div>
<div class="line"><a name="l00680"></a><span class="lineno"> 680</span>  fit_function.f = (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> (*)(<span class="keyword">const</span> gsl_vector* x, <span class="keywordtype">void</span>* params, gsl_vector* f)) & <a class="code" href="classOpenMS_1_1TwoDOptimization.html#aa82b642dc0b200f292a5f44e6458bf16">OpenMS::TwoDOptimization::residual2D_</a>;</div>
<div class="line"><a name="l00681"></a><span class="lineno"> 681</span>  fit_function.df = (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> (*)(<span class="keyword">const</span> gsl_vector* x, <span class="keywordtype">void</span>* params, gsl_matrix* J)) & <a class="code" href="classOpenMS_1_1TwoDOptimization.html#ab25862b6e7eaee9e6739c52ae57d0896">OpenMS::TwoDOptimization::jacobian2D_</a>;</div>
<div class="line"><a name="l00682"></a><span class="lineno"> 682</span>  fit_function.fdf = (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> (*)(<span class="keyword">const</span> gsl_vector* x, <span class="keywordtype">void</span>* params, gsl_vector* f, gsl_matrix* J)) & <a class="code" href="classOpenMS_1_1TwoDOptimization.html#af4c776b75fd26c91f570e5bb9ef0b4c4">OpenMS::TwoDOptimization::evaluate2D_</a>;</div>
<div class="line"><a name="l00683"></a><span class="lineno"> 683</span>  <span class="comment">// gsl crashes when n is smaller than p!</span></div>
<div class="line"><a name="l00684"></a><span class="lineno"> 684</span>  fit_function.n = std::max(num_positions + 1, (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>)(nr_parameters));</div>
<div class="line"><a name="l00685"></a><span class="lineno"> 685</span>  fit_function.p = nr_parameters;</div>
<div class="line"><a name="l00686"></a><span class="lineno"> 686</span>  fit_function.params = &d;</div>
<div class="line"><a name="l00687"></a><span class="lineno"> 687</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00688"></a><span class="lineno"> 688</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"fit_function.n "</span> << fit_function.n</div>
<div class="line"><a name="l00689"></a><span class="lineno"> 689</span>  << <span class="stringliteral">"\tfit_function.p "</span> << fit_function.p << std::endl;</div>
<div class="line"><a name="l00690"></a><span class="lineno"> 690</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00691"></a><span class="lineno"> 691</span> <span class="preprocessor"></span> <span class="keyword">const</span> gsl_multifit_fdfsolver_type* type = gsl_multifit_fdfsolver_lmsder;</div>
<div class="line"><a name="l00692"></a><span class="lineno"> 692</span> </div>
<div class="line"><a name="l00693"></a><span class="lineno"> 693</span>  gsl_multifit_fdfsolver* fit = gsl_multifit_fdfsolver_alloc(type,</div>
<div class="line"><a name="l00694"></a><span class="lineno"> 694</span>  std::max(num_positions + 1, (<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>)(nr_parameters)),</div>
<div class="line"><a name="l00695"></a><span class="lineno"> 695</span>  nr_parameters);</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>  gsl_multifit_fdfsolver_set(fit, &fit_function, start_value);</div>
<div class="line"><a name="l00698"></a><span class="lineno"> 698</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> </div>
<div class="line"><a name="l00701"></a><span class="lineno"> 701</span>  <span class="comment">// initial norm</span></div>
<div class="line"><a name="l00702"></a><span class="lineno"> 702</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00703"></a><span class="lineno"> 703</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"Before optimization: ||f|| = "</span> << gsl_blas_dnrm2(fit->f) << std::endl;</div>
<div class="line"><a name="l00704"></a><span class="lineno"> 704</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00705"></a><span class="lineno"> 705</span> <span class="preprocessor"></span> <span class="comment">// Iteration</span></div>
<div class="line"><a name="l00706"></a><span class="lineno"> 706</span>  <a class="code" href="classunsigned_01int.html">UInt</a> iteration = 0;</div>
<div class="line"><a name="l00707"></a><span class="lineno"> 707</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> status;</div>
<div class="line"><a name="l00708"></a><span class="lineno"> 708</span> </div>
<div class="line"><a name="l00709"></a><span class="lineno"> 709</span>  <span class="keywordflow">do</span></div>
<div class="line"><a name="l00710"></a><span class="lineno"> 710</span>  {</div>
<div class="line"><a name="l00711"></a><span class="lineno"> 711</span>  iteration++;</div>
<div class="line"><a name="l00712"></a><span class="lineno"> 712</span>  status = gsl_multifit_fdfsolver_iterate(fit);</div>
<div class="line"><a name="l00713"></a><span class="lineno"> 713</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00714"></a><span class="lineno"> 714</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"Iteration "</span> << iteration << <span class="stringliteral">"; Status "</span> << gsl_strerror(status) << <span class="stringliteral">"; "</span> << std::endl;</div>
<div class="line"><a name="l00715"></a><span class="lineno"> 715</span>  std::cout << <span class="stringliteral">"||f|| = "</span> << gsl_blas_dnrm2(fit->f) << std::endl;</div>
<div class="line"><a name="l00716"></a><span class="lineno"> 716</span>  std::cout << <span class="stringliteral">"Number of parms: "</span> << nr_parameters << std::endl;</div>
<div class="line"><a name="l00717"></a><span class="lineno"> 717</span>  std::cout << <span class="stringliteral">"Delta: "</span> << gsl_blas_dnrm2(fit->dx) << std::endl;</div>
<div class="line"><a name="l00718"></a><span class="lineno"> 718</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00719"></a><span class="lineno"> 719</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00720"></a><span class="lineno"> 720</span>  status = gsl_multifit_test_delta(fit->dx, fit->x, <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a1ba9944277216253f5225aa74581147e">eps_abs_</a>, <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0409337ea8ad2ae8fde8f6cba1e889a2">eps_rel_</a>);</div>
<div class="line"><a name="l00721"></a><span class="lineno"> 721</span>  <span class="keywordflow">if</span> (status != GSL_CONTINUE)</div>
<div class="line"><a name="l00722"></a><span class="lineno"> 722</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00723"></a><span class="lineno"> 723</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>  <span class="keywordflow">while</span> (status == GSL_CONTINUE && iteration < <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a78c0d505b8706df48e8cf696e21035ee">max_iteration_</a>);</div>
<div class="line"><a name="l00726"></a><span class="lineno"> 726</span> </div>
<div class="line"><a name="l00727"></a><span class="lineno"> 727</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00728"></a><span class="lineno"> 728</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"Finished! No. of iterations"</span> << iteration << std::endl;</div>
<div class="line"><a name="l00729"></a><span class="lineno"> 729</span>  std::cout << <span class="stringliteral">"Delta: "</span> << gsl_blas_dnrm2(fit->dx) << std::endl;</div>
<div class="line"><a name="l00730"></a><span class="lineno"> 730</span>  <a class="code" href="classdouble.html">DoubleReal</a> chi = gsl_blas_dnrm2(fit->f);</div>
<div class="line"><a name="l00731"></a><span class="lineno"> 731</span>  std::cout << <span class="stringliteral">"After optimization: || f || = "</span> << gsl_blas_dnrm2(fit->f) << std::endl;</div>
<div class="line"><a name="l00732"></a><span class="lineno"> 732</span>  std::cout << <span class="stringliteral">"chisq/dof = "</span> << pow(chi, 2.0) / (num_positions - nr_parameters);</div>
<div class="line"><a name="l00733"></a><span class="lineno"> 733</span> </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>  std::cout << <span class="stringliteral">"----------------------------------------------\n\nnachher"</span> << std::endl;</div>
<div class="line"><a name="l00736"></a><span class="lineno"> 736</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> = 0; <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a> < fit->x->size; ++<a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>)</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>  std::cout << gsl_vector_get(fit->x, <a class="code" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">k</a>) << std::endl;</div>
<div class="line"><a name="l00739"></a><span class="lineno"> 739</span>  }</div>
<div class="line"><a name="l00740"></a><span class="lineno"> 740</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00741"></a><span class="lineno"> 741</span> <span class="preprocessor"></span> <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> peak_idx = 0;</div>
<div class="line"><a name="l00742"></a><span class="lineno"> 742</span>  std::map<Int, std::vector<PeakIndex> >::iterator itv</div>
<div class="line"><a name="l00743"></a><span class="lineno"> 743</span>  = d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a1e60993834d6cab4067738dfd729dad0">matching_peaks</a>.begin();</div>
<div class="line"><a name="l00744"></a><span class="lineno"> 744</span>  <span class="keywordflow">for</span> (; itv != d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a1e60993834d6cab4067738dfd729dad0">matching_peaks</a>.end(); ++itv)</div>
<div class="line"><a name="l00745"></a><span class="lineno"> 745</span>  {</div>
<div class="line"><a name="l00746"></a><span class="lineno"> 746</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> i = distance(d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a1e60993834d6cab4067738dfd729dad0">matching_peaks</a>.begin(), itv);</div>
<div class="line"><a name="l00747"></a><span class="lineno"> 747</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j < itv->second.size(); ++j)</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> </div>
<div class="line"><a name="l00750"></a><span class="lineno"> 750</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00751"></a><span class="lineno"> 751</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"pos: "</span> << itv->second[j].getPeak(ms_exp).getMZ() << <span class="stringliteral">"\nint: "</span> << itv->second[j].getSpectrum(ms_exp).getFloatDataArrays()[1][itv->second[j].peak] <span class="comment">//itv->second[j].getPeak(ms_exp).getIntensity()</span></div>
<div class="line"><a name="l00752"></a><span class="lineno"> 752</span>  << <span class="stringliteral">"\nlw: "</span> << itv->second[j].getSpectrum(ms_exp).getFloatDataArrays()[3][itv->second[j].peak]</div>
<div class="line"><a name="l00753"></a><span class="lineno"> 753</span>  << <span class="stringliteral">"\nrw: "</span> << itv->second[j].getSpectrum(ms_exp).getFloatDataArrays()[4][itv->second[j].peak] << <span class="stringliteral">"\n"</span>;</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> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00756"></a><span class="lineno"> 756</span> <span class="preprocessor"></span> <a class="code" href="classdouble.html">DoubleReal</a> mz = gsl_vector_get(fit->x, d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a9d5caa74a619fd37c7352fce078259fd">total_nr_peaks</a> + 3 * i);</div>
<div class="line"><a name="l00757"></a><span class="lineno"> 757</span>  ms_exp[itv->second[j].spectrum][itv->second[j].peak].setMZ(mz);</div>
<div class="line"><a name="l00758"></a><span class="lineno"> 758</span>  <a class="code" href="classdouble.html">DoubleReal</a> height = (gsl_vector_get(fit->x, peak_idx));</div>
<div class="line"><a name="l00759"></a><span class="lineno"> 759</span>  ms_exp[itv->second[j].spectrum].getFloatDataArrays()[1][itv->second[j].peak] = height;</div>
<div class="line"><a name="l00760"></a><span class="lineno"> 760</span>  <a class="code" href="classdouble.html">DoubleReal</a> left_width = gsl_vector_get(fit->x, d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a9d5caa74a619fd37c7352fce078259fd">total_nr_peaks</a> + 3 * i + 1);</div>
<div class="line"><a name="l00761"></a><span class="lineno"> 761</span>  ms_exp[itv->second[j].spectrum].getFloatDataArrays()[3][itv->second[j].peak] = left_width;</div>
<div class="line"><a name="l00762"></a><span class="lineno"> 762</span>  <a class="code" href="classdouble.html">DoubleReal</a> right_width = gsl_vector_get(fit->x, d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a9d5caa74a619fd37c7352fce078259fd">total_nr_peaks</a> + 3 * i + 2);</div>
<div class="line"><a name="l00763"></a><span class="lineno"> 763</span>  ms_exp[itv->second[j].spectrum].getFloatDataArrays()[4][itv->second[j].peak] = right_width;</div>
<div class="line"><a name="l00764"></a><span class="lineno"> 764</span>  <span class="comment">// calculate area</span></div>
<div class="line"><a name="l00765"></a><span class="lineno"> 765</span>  <span class="keywordflow">if</span> ((<a class="code" href="structOpenMS_1_1PeakShape.html#a1d1cfd8ffb84e947f82999c682b666a7">PeakShape::Type</a>)(<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>)ms_exp[itv->second[j].spectrum].getFloatDataArrays()[5][itv->second[j].peak] == <a class="code" href="structOpenMS_1_1PeakShape.html#a1d1cfd8ffb84e947f82999c682b666a7a6ba0b50b9f0f84a5ad13827c57240f76">PeakShape::LORENTZ_PEAK</a>)</div>
<div class="line"><a name="l00766"></a><span class="lineno"> 766</span>  {</div>
<div class="line"><a name="l00767"></a><span class="lineno"> 767</span>  <a class="code" href="classdouble.html">DoubleReal</a> x_left_endpoint = mz - 1 / left_width* sqrt(height / 1 - 1);</div>
<div class="line"><a name="l00768"></a><span class="lineno"> 768</span>  <a class="code" href="classdouble.html">DoubleReal</a> x_rigth_endpoint = mz + 1 / right_width* sqrt(height / 1 - 1);</div>
<div class="line"><a name="l00769"></a><span class="lineno"> 769</span>  <a class="code" href="classdouble.html">DoubleReal</a> area_left = -height / left_width* atan(left_width * (x_left_endpoint - mz));</div>
<div class="line"><a name="l00770"></a><span class="lineno"> 770</span>  <a class="code" href="classdouble.html">DoubleReal</a> area_right = -height / right_width* atan(right_width * (mz - x_rigth_endpoint));</div>
<div class="line"><a name="l00771"></a><span class="lineno"> 771</span>  ms_exp[itv->second[j].spectrum][itv->second[j].peak].setIntensity(area_left + area_right);</div>
<div class="line"><a name="l00772"></a><span class="lineno"> 772</span>  }</div>
<div class="line"><a name="l00773"></a><span class="lineno"> 773</span>  <span class="keywordflow">else</span> <span class="comment">// it's a sech peak</span></div>
<div class="line"><a name="l00774"></a><span class="lineno"> 774</span>  {</div>
<div class="line"><a name="l00775"></a><span class="lineno"> 775</span>  <a class="code" href="classdouble.html">DoubleReal</a> x_left_endpoint = mz - 1 / left_width* boost::math::acosh(sqrt(height / 0.001));</div>
<div class="line"><a name="l00776"></a><span class="lineno"> 776</span>  <a class="code" href="classdouble.html">DoubleReal</a> x_rigth_endpoint = mz + 1 / right_width* boost::math::acosh(sqrt(height / 0.001));</div>
<div class="line"><a name="l00777"></a><span class="lineno"> 777</span>  <a class="code" href="classdouble.html">DoubleReal</a> area_left = -height / left_width * (sinh(left_width * (mz - x_left_endpoint)) / cosh(left_width * (mz - x_left_endpoint)));</div>
<div class="line"><a name="l00778"></a><span class="lineno"> 778</span>  <a class="code" href="classdouble.html">DoubleReal</a> area_right = -height / right_width * (sinh(right_width * (mz - x_rigth_endpoint)) / cosh(right_width * (mz - x_rigth_endpoint)));</div>
<div class="line"><a name="l00779"></a><span class="lineno"> 779</span>  ms_exp[itv->second[j].spectrum][itv->second[j].peak].setIntensity(area_left + area_right);</div>
<div class="line"><a name="l00780"></a><span class="lineno"> 780</span>  }</div>
<div class="line"><a name="l00781"></a><span class="lineno"> 781</span> </div>
<div class="line"><a name="l00782"></a><span class="lineno"> 782</span> </div>
<div class="line"><a name="l00783"></a><span class="lineno"> 783</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00784"></a><span class="lineno"> 784</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"pos: "</span> << itv->second[j].getPeak(ms_exp).getMZ() << <span class="stringliteral">"\nint: "</span> << itv->second[j].getSpectrum(ms_exp).getFloatDataArrays()[1][itv->second[j].peak] <span class="comment">//itv->second[j].getPeak(ms_exp).getIntensity()</span></div>
<div class="line"><a name="l00785"></a><span class="lineno"> 785</span>  << <span class="stringliteral">"\nlw: "</span> << itv->second[j].getSpectrum(ms_exp).getFloatDataArrays()[3][itv->second[j].peak]</div>
<div class="line"><a name="l00786"></a><span class="lineno"> 786</span>  << <span class="stringliteral">"\nrw: "</span> << itv->second[j].getSpectrum(ms_exp).getFloatDataArrays()[4][itv->second[j].peak] << <span class="stringliteral">"\n"</span>;</div>
<div class="line"><a name="l00787"></a><span class="lineno"> 787</span> </div>
<div class="line"><a name="l00788"></a><span class="lineno"> 788</span> <span class="comment">// std::cout << "pos: "<<itv->second[j]->getMZ()<<"\nint: "<<itv->second[j]->getIntensity()</span></div>
<div class="line"><a name="l00789"></a><span class="lineno"> 789</span> <span class="comment">// <<"\nlw: "<<itv->second[j]->getLeftWidthParameter()</span></div>
<div class="line"><a name="l00790"></a><span class="lineno"> 790</span> <span class="comment">// <<"\nrw: "<<itv->second[j]->getRightWidthParameter() << "\n";</span></div>
<div class="line"><a name="l00791"></a><span class="lineno"> 791</span> </div>
<div class="line"><a name="l00792"></a><span class="lineno"> 792</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00793"></a><span class="lineno"> 793</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00794"></a><span class="lineno"> 794</span>  ++peak_idx;</div>
<div class="line"><a name="l00795"></a><span class="lineno"> 795</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>  }</div>
<div class="line"><a name="l00798"></a><span class="lineno"> 798</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>  gsl_multifit_fdfsolver_free(fit);</div>
<div class="line"><a name="l00801"></a><span class="lineno"> 801</span>  gsl_vector_free(start_value);</div>
<div class="line"><a name="l00802"></a><span class="lineno"> 802</span>  ++counter;</div>
<div class="line"><a name="l00803"></a><span class="lineno"> 803</span>  } <span class="comment">// end for</span></div>
<div class="line"><a name="l00804"></a><span class="lineno"> 804</span>  <span class="comment">//#undef DEBUG_2D</span></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> </div>
<div class="line"><a name="l00807"></a><span class="lineno"> 807</span>  <span class="keyword">template</span> <<span class="keyword">typename</span> InputSpectrumIterator, <span class="keyword">typename</span> OutputPeakType></div>
<div class="line"><a name="l00808"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#adca2617ab638fed2467b9d57b1fe2cfa"> 808</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#adca2617ab638fed2467b9d57b1fe2cfa">TwoDOptimization::optimizeRegionsScanwise_</a>(InputSpectrumIterator& first,</div>
<div class="line"><a name="l00809"></a><span class="lineno"> 809</span>  InputSpectrumIterator& last,</div>
<div class="line"><a name="l00810"></a><span class="lineno"> 810</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<OutputPeakType></a>& ms_exp)</div>
<div class="line"><a name="l00811"></a><span class="lineno"> 811</span>  {</div>
<div class="line"><a name="l00812"></a><span class="lineno"> 812</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> counter = 0;</div>
<div class="line"><a name="l00813"></a><span class="lineno"> 813</span>  <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html">TwoDOptimization::Data</a> d;</div>
<div class="line"><a name="l00814"></a><span class="lineno"> 814</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a2dcab4dd664c2b08f478ebde32edaa74">picked_peaks</a> = ms_exp;</div>
<div class="line"><a name="l00815"></a><span class="lineno"> 815</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a16930394d61d06ff8227219211874592">raw_data_first</a> = first;</div>
<div class="line"><a name="l00816"></a><span class="lineno"> 816</span> </div>
<div class="line"><a name="l00817"></a><span class="lineno"> 817</span>  <span class="comment">//std::cout << "richtig hier" << std::endl;</span></div>
<div class="line"><a name="l00818"></a><span class="lineno"> 818</span>  <span class="keyword">struct </span><a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">OpenMS::OptimizationFunctions::PenaltyFactors</a> penalties;</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>  <a class="code" href="classOpenMS_1_1DataValue.html">DataValue</a> dv = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"penalties:position"</span>);</div>
<div class="line"><a name="l00822"></a><span class="lineno"> 822</span>  <span class="keywordflow">if</span> (dv.isEmpty() || dv.toString() == <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00823"></a><span class="lineno"> 823</span>  penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a5e9dd75fc35bca3ebe4981821077aebe">pos</a> = 0.;</div>
<div class="line"><a name="l00824"></a><span class="lineno"> 824</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00825"></a><span class="lineno"> 825</span>  penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a5e9dd75fc35bca3ebe4981821077aebe">pos</a> = (<span class="keywordtype">float</span>)dv;</div>
<div class="line"><a name="l00826"></a><span class="lineno"> 826</span> </div>
<div class="line"><a name="l00827"></a><span class="lineno"> 827</span>  dv = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"penalties:left_width"</span>);</div>
<div class="line"><a name="l00828"></a><span class="lineno"> 828</span>  <span class="keywordflow">if</span> (dv.isEmpty() || dv.toString() == <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00829"></a><span class="lineno"> 829</span>  penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#abb10592f0ea83f824c0a14f4afa95be4">lWidth</a> = 1.;</div>
<div class="line"><a name="l00830"></a><span class="lineno"> 830</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00831"></a><span class="lineno"> 831</span>  penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#abb10592f0ea83f824c0a14f4afa95be4">lWidth</a> = (<span class="keywordtype">float</span>)dv;</div>
<div class="line"><a name="l00832"></a><span class="lineno"> 832</span> </div>
<div class="line"><a name="l00833"></a><span class="lineno"> 833</span>  dv = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"penalties:right_width"</span>);</div>
<div class="line"><a name="l00834"></a><span class="lineno"> 834</span>  <span class="keywordflow">if</span> (dv.isEmpty() || dv.toString() == <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00835"></a><span class="lineno"> 835</span>  penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a478a632c0b5a363e215061428eee1a1c">rWidth</a> = 1.;</div>
<div class="line"><a name="l00836"></a><span class="lineno"> 836</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00837"></a><span class="lineno"> 837</span>  penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a478a632c0b5a363e215061428eee1a1c">rWidth</a> = (<span class="keywordtype">float</span>)dv;</div>
<div class="line"><a name="l00838"></a><span class="lineno"> 838</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00839"></a><span class="lineno"> 839</span> <span class="preprocessor"></span> std::cout << penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a5e9dd75fc35bca3ebe4981821077aebe">pos</a> << <span class="stringliteral">" "</span></div>
<div class="line"><a name="l00840"></a><span class="lineno"> 840</span>  << penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a478a632c0b5a363e215061428eee1a1c">rWidth</a> << <span class="stringliteral">" "</span></div>
<div class="line"><a name="l00841"></a><span class="lineno"> 841</span>  << penalties.<a class="code" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#abb10592f0ea83f824c0a14f4afa95be4">lWidth</a> << std::endl;</div>
<div class="line"><a name="l00842"></a><span class="lineno"> 842</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00843"></a><span class="lineno"> 843</span> <span class="preprocessor"></span><span class="comment">// MSExperiment<Peak1D >::const_iterator help = first;</span></div>
<div class="line"><a name="l00844"></a><span class="lineno"> 844</span> <span class="comment">// // std::cout << "\n\n\n\n---------------------------------------------------------------";</span></div>
<div class="line"><a name="l00845"></a><span class="lineno"> 845</span> <span class="comment">// while(help!=last)</span></div>
<div class="line"><a name="l00846"></a><span class="lineno"> 846</span> <span class="comment">// {</span></div>
<div class="line"><a name="l00847"></a><span class="lineno"> 847</span> <span class="comment">// // std::cout<<help->getRT()<<std::endl;</span></div>
<div class="line"><a name="l00848"></a><span class="lineno"> 848</span> <span class="comment">// ++help;</span></div>
<div class="line"><a name="l00849"></a><span class="lineno"> 849</span> <span class="comment">// }</span></div>
<div class="line"><a name="l00850"></a><span class="lineno"> 850</span>  <span class="comment">// std::cout << "---------------------------------------------------------------\n\n\n\n";</span></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>  <a class="code" href="classunsigned_01int.html">UInt</a> max_iteration;</div>
<div class="line"><a name="l00853"></a><span class="lineno"> 853</span>  dv = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"iterations"</span>);</div>
<div class="line"><a name="l00854"></a><span class="lineno"> 854</span>  <span class="keywordflow">if</span> (dv.isEmpty() || dv.toString() == <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00855"></a><span class="lineno"> 855</span>  max_iteration = 15;</div>
<div class="line"><a name="l00856"></a><span class="lineno"> 856</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00857"></a><span class="lineno"> 857</span>  max_iteration = (<a class="code" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a>)dv;</div>
<div class="line"><a name="l00858"></a><span class="lineno"> 858</span> </div>
<div class="line"><a name="l00859"></a><span class="lineno"> 859</span>  <a class="code" href="classdouble.html">DoubleReal</a> eps_abs;</div>
<div class="line"><a name="l00860"></a><span class="lineno"> 860</span>  dv = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"delta_abs_error"</span>);</div>
<div class="line"><a name="l00861"></a><span class="lineno"> 861</span>  <span class="keywordflow">if</span> (dv.isEmpty() || dv.toString() == <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00862"></a><span class="lineno"> 862</span>  eps_abs = 1e-04f;</div>
<div class="line"><a name="l00863"></a><span class="lineno"> 863</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00864"></a><span class="lineno"> 864</span>  eps_abs = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)dv;</div>
<div class="line"><a name="l00865"></a><span class="lineno"> 865</span> </div>
<div class="line"><a name="l00866"></a><span class="lineno"> 866</span>  <a class="code" href="classdouble.html">DoubleReal</a> eps_rel;</div>
<div class="line"><a name="l00867"></a><span class="lineno"> 867</span>  dv = <a class="code" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a>.<a class="code" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">getValue</a>(<span class="stringliteral">"delta_rel_error"</span>);</div>
<div class="line"><a name="l00868"></a><span class="lineno"> 868</span>  <span class="keywordflow">if</span> (dv.isEmpty() || dv.toString() == <span class="stringliteral">""</span>)</div>
<div class="line"><a name="l00869"></a><span class="lineno"> 869</span>  eps_rel = 1e-04f;</div>
<div class="line"><a name="l00870"></a><span class="lineno"> 870</span>  <span class="keywordflow">else</span></div>
<div class="line"><a name="l00871"></a><span class="lineno"> 871</span>  eps_rel = (<a class="code" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>)dv;</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>  std::vector<PeakShape> peak_shapes;</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> </div>
<div class="line"><a name="l00876"></a><span class="lineno"> 876</span>  <span class="comment">// go through the clusters</span></div>
<div class="line"><a name="l00877"></a><span class="lineno"> 877</span>  <span class="keywordflow">for</span> (std::multimap<DoubleReal, IsotopeCluster>::iterator it = <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a>.begin();</div>
<div class="line"><a name="l00878"></a><span class="lineno"> 878</span>  it != <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a>.end();</div>
<div class="line"><a name="l00879"></a><span class="lineno"> 879</span>  ++it)</div>
<div class="line"><a name="l00880"></a><span class="lineno"> 880</span>  {</div>
<div class="line"><a name="l00881"></a><span class="lineno"> 881</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">iso_map_iter</a> = it;</div>
<div class="line"><a name="l00882"></a><span class="lineno"> 882</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00883"></a><span class="lineno"> 883</span> <span class="preprocessor"></span> std::cerr << <span class="stringliteral">"element: "</span> << counter << std::endl;</div>
<div class="line"><a name="l00884"></a><span class="lineno"> 884</span>  std::cerr << <span class="stringliteral">"mz: "</span> << it->first << std::endl << <span class="stringliteral">"rts: "</span>;</div>
<div class="line"><a name="l00885"></a><span class="lineno"> 885</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < it->second.scans.size(); ++i)</div>
<div class="line"><a name="l00886"></a><span class="lineno"> 886</span>  std::cerr << it->second.scans[i] << <span class="stringliteral">"\n"</span>;</div>
<div class="line"><a name="l00887"></a><span class="lineno"> 887</span>  std::cerr << std::endl << <span class="stringliteral">"peaks: "</span>;</div>
<div class="line"><a name="l00888"></a><span class="lineno"> 888</span>  IsotopeCluster::IndexSet::const_iterator iter = it->second.peaks.begin();</div>
<div class="line"><a name="l00889"></a><span class="lineno"> 889</span>  <span class="keywordflow">for</span> (; iter != it->second.peaks.end(); ++iter)</div>
<div class="line"><a name="l00890"></a><span class="lineno"> 890</span>  std::cerr << ms_exp[iter->first].getRT() << <span class="stringliteral">" "</span> << (ms_exp[iter->first][iter->second]).getMZ() << std::endl;</div>
<div class="line"><a name="l00891"></a><span class="lineno"> 891</span>  <span class="comment">//for(Size i=0;i<it->second.peaks_.size();++i) std::cout << ms_exp[it->first].getRT() << " "<<(ms_exp[it->first][it->second]).getMZ()<<std::endl;</span></div>
<div class="line"><a name="l00892"></a><span class="lineno"> 892</span>  std::cerr << std::endl << std::endl;</div>
<div class="line"><a name="l00893"></a><span class="lineno"> 893</span> </div>
<div class="line"><a name="l00894"></a><span class="lineno"> 894</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00895"></a><span class="lineno"> 895</span> <span class="preprocessor"></span> <span class="comment">// prepare for optimization:</span></div>
<div class="line"><a name="l00896"></a><span class="lineno"> 896</span>  <span class="comment">// determine the matching peaks</span></div>
<div class="line"><a name="l00897"></a><span class="lineno"> 897</span>  <span class="comment">// and the endpoints of each isotope pattern in the cluster</span></div>
<div class="line"><a name="l00898"></a><span class="lineno"> 898</span> </div>
<div class="line"><a name="l00899"></a><span class="lineno"> 899</span>  <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a6d2b21b20b10f65e5a6052e8c8aa84e7">getRegionEndpoints_</a>(ms_exp, first, last, counter, 400, d);</div>
<div class="line"><a name="l00900"></a><span class="lineno"> 900</span>  <a class="code" href="structOpenMS_1_1OptimizePick_1_1Data.html">OptimizePick::Data</a> data;</div>
<div class="line"><a name="l00901"></a><span class="lineno"> 901</span> </div>
<div class="line"><a name="l00902"></a><span class="lineno"> 902</span> </div>
<div class="line"><a name="l00903"></a><span class="lineno"> 903</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> idx = 0;</div>
<div class="line"><a name="l00904"></a><span class="lineno"> 904</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>.size() / 2; ++i)</div>
<div class="line"><a name="l00905"></a><span class="lineno"> 905</span>  {</div>
<div class="line"><a name="l00906"></a><span class="lineno"> 906</span>  data.<a class="code" href="structOpenMS_1_1OptimizePick_1_1Data.html#a649cc300c964845ccc272fd2229b6ed4">positions</a>.clear();</div>
<div class="line"><a name="l00907"></a><span class="lineno"> 907</span>  data.<a class="code" href="structOpenMS_1_1OptimizePick_1_1Data.html#afc5753d32dfc3c8659038a3e1ac68c86">signal</a>.clear();</div>
<div class="line"><a name="l00908"></a><span class="lineno"> 908</span> </div>
<div class="line"><a name="l00909"></a><span class="lineno"> 909</span>  <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<Peak1D>::SpectrumType::const_iterator</a> ms_it =</div>
<div class="line"><a name="l00910"></a><span class="lineno"> 910</span>  (d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a16930394d61d06ff8227219211874592">raw_data_first</a> + d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>[2 * i].first)->begin() + d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>[2 * i].second;</div>
<div class="line"><a name="l00911"></a><span class="lineno"> 911</span>  <a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> size = distance(ms_it, (d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a16930394d61d06ff8227219211874592">raw_data_first</a> + d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>[2 * i].first)-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>() + d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>[2 * i + 1].second);</div>
<div class="line"><a name="l00912"></a><span class="lineno"> 912</span>  data.<a class="code" href="structOpenMS_1_1OptimizePick_1_1Data.html#a649cc300c964845ccc272fd2229b6ed4">positions</a>.reserve(size);</div>
<div class="line"><a name="l00913"></a><span class="lineno"> 913</span>  data.<a class="code" href="structOpenMS_1_1OptimizePick_1_1Data.html#afc5753d32dfc3c8659038a3e1ac68c86">signal</a>.reserve(size);</div>
<div class="line"><a name="l00914"></a><span class="lineno"> 914</span> </div>
<div class="line"><a name="l00915"></a><span class="lineno"> 915</span>  <span class="keywordflow">while</span> (ms_it != (d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a16930394d61d06ff8227219211874592">raw_data_first</a> + d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>[2 * i].first)-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>() + d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>[2 * i + 1].second)</div>
<div class="line"><a name="l00916"></a><span class="lineno"> 916</span>  {</div>
<div class="line"><a name="l00917"></a><span class="lineno"> 917</span>  data.<a class="code" href="structOpenMS_1_1OptimizePick_1_1Data.html#a649cc300c964845ccc272fd2229b6ed4">positions</a>.push_back(ms_it->getMZ());</div>
<div class="line"><a name="l00918"></a><span class="lineno"> 918</span>  data.<a class="code" href="structOpenMS_1_1OptimizePick_1_1Data.html#afc5753d32dfc3c8659038a3e1ac68c86">signal</a>.push_back(ms_it->getIntensity());</div>
<div class="line"><a name="l00919"></a><span class="lineno"> 919</span>  ++ms_it;</div>
<div class="line"><a name="l00920"></a><span class="lineno"> 920</span>  }</div>
<div class="line"><a name="l00921"></a><span class="lineno"> 921</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>  <a class="code" href="structOpenMS_1_1IsotopeCluster.html#a0cab124671a3ada269f0553e1c8934da">IsotopeCluster::IndexPair</a> pair;</div>
<div class="line"><a name="l00924"></a><span class="lineno"> 924</span>  pair.first = d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">iso_map_iter</a>->second.peaks.begin()->first + idx;</div>
<div class="line"><a name="l00925"></a><span class="lineno"> 925</span> </div>
<div class="line"><a name="l00926"></a><span class="lineno"> 926</span>  IsotopeCluster::IndexSet::const_iterator set_iter = lower_bound(d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">iso_map_iter</a>->second.peaks.begin(),</div>
<div class="line"><a name="l00927"></a><span class="lineno"> 927</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">iso_map_iter</a>->second.peaks.end(),</div>
<div class="line"><a name="l00928"></a><span class="lineno"> 928</span>  pair, <a class="code" href="structOpenMS_1_1PairComparatorFirstElement.html">PairComparatorFirstElement<IsotopeCluster::IndexPair></a>());</div>
<div class="line"><a name="l00929"></a><span class="lineno"> 929</span> </div>
<div class="line"><a name="l00930"></a><span class="lineno"> 930</span> </div>
<div class="line"><a name="l00931"></a><span class="lineno"> 931</span>  <span class="comment">// find the last entry with this rt-value</span></div>
<div class="line"><a name="l00932"></a><span class="lineno"> 932</span>  ++pair.first;</div>
<div class="line"><a name="l00933"></a><span class="lineno"> 933</span>  IsotopeCluster::IndexSet::const_iterator set_iter2 = lower_bound(d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">iso_map_iter</a>->second.peaks.begin(),</div>
<div class="line"><a name="l00934"></a><span class="lineno"> 934</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">iso_map_iter</a>->second.peaks.end(),</div>
<div class="line"><a name="l00935"></a><span class="lineno"> 935</span>  pair, <a class="code" href="structOpenMS_1_1PairComparatorFirstElement.html">PairComparatorFirstElement<IsotopeCluster::IndexPair></a>());</div>
<div class="line"><a name="l00936"></a><span class="lineno"> 936</span> </div>
<div class="line"><a name="l00937"></a><span class="lineno"> 937</span>  <span class="keywordflow">while</span> (set_iter != set_iter2)</div>
<div class="line"><a name="l00938"></a><span class="lineno"> 938</span>  {</div>
<div class="line"><a name="l00939"></a><span class="lineno"> 939</span>  <span class="keyword">const</span> <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> peak_index = set_iter->second;</div>
<div class="line"><a name="l00940"></a><span class="lineno"> 940</span>  <span class="keyword">const</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a>& spec = ms_exp[set_iter->first];</div>
<div class="line"><a name="l00941"></a><span class="lineno"> 941</span>  <a class="code" href="structOpenMS_1_1PeakShape.html">PeakShape</a> shape(spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>()[1][peak_index], <span class="comment">//intensity</span></div>
<div class="line"><a name="l00942"></a><span class="lineno"> 942</span>  spec[peak_index].getMZ(),</div>
<div class="line"><a name="l00943"></a><span class="lineno"> 943</span>  spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>()[3][peak_index], <span class="comment">//left width</span></div>
<div class="line"><a name="l00944"></a><span class="lineno"> 944</span>  spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>()[4][peak_index], <span class="comment">//right width</span></div>
<div class="line"><a name="l00945"></a><span class="lineno"> 945</span>  spec[peak_index].getIntensity(), <span class="comment">//area is stored in peak intensity</span></div>
<div class="line"><a name="l00946"></a><span class="lineno"> 946</span>  std::vector<Peak1D>::iterator(),</div>
<div class="line"><a name="l00947"></a><span class="lineno"> 947</span>  std::vector<Peak1D>::iterator(),</div>
<div class="line"><a name="l00948"></a><span class="lineno"> 948</span>  <a class="code" href="structOpenMS_1_1PeakShape.html#a1d1cfd8ffb84e947f82999c682b666a7">PeakShape::Type</a>(<a class="code" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>(spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>()[5][peak_index]))); <span class="comment">//shape</span></div>
<div class="line"><a name="l00949"></a><span class="lineno"> 949</span>  peak_shapes.push_back(shape);</div>
<div class="line"><a name="l00950"></a><span class="lineno"> 950</span>  ++set_iter;</div>
<div class="line"><a name="l00951"></a><span class="lineno"> 951</span>  }</div>
<div class="line"><a name="l00952"></a><span class="lineno"> 952</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00953"></a><span class="lineno"> 953</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"rt "</span></div>
<div class="line"><a name="l00954"></a><span class="lineno"> 954</span>  << (d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a16930394d61d06ff8227219211874592">raw_data_first</a> + d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>[2 * i].first)->getRT()</div>
<div class="line"><a name="l00955"></a><span class="lineno"> 955</span>  << <span class="stringliteral">"\n"</span>;</div>
<div class="line"><a name="l00956"></a><span class="lineno"> 956</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00957"></a><span class="lineno"> 957</span> <span class="preprocessor"></span> <a class="code" href="classOpenMS_1_1OptimizePick.html">OptimizePick</a> opt(penalties, max_iteration, eps_abs, eps_rel);</div>
<div class="line"><a name="l00958"></a><span class="lineno"> 958</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00959"></a><span class="lineno"> 959</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"vorher\n"</span>;</div>
<div class="line"><a name="l00960"></a><span class="lineno"> 960</span> </div>
<div class="line"><a name="l00961"></a><span class="lineno"> 961</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p < peak_shapes.size(); ++p)</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>  std::cout << peak_shapes[p].mz_position << <span class="stringliteral">"\t"</span> << peak_shapes[p].height</div>
<div class="line"><a name="l00964"></a><span class="lineno"> 964</span>  << <span class="stringliteral">"\t"</span> << peak_shapes[p].left_width << <span class="stringliteral">"\t"</span> << peak_shapes[p].right_width << std::endl;</div>
<div class="line"><a name="l00965"></a><span class="lineno"> 965</span>  }</div>
<div class="line"><a name="l00966"></a><span class="lineno"> 966</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00967"></a><span class="lineno"> 967</span> <span class="preprocessor"></span> opt.<a class="code" href="classOpenMS_1_1OptimizePick.html#ae69ba4a78f94acc6d88ec067397bf490">optimize</a>(peak_shapes, data);</div>
<div class="line"><a name="l00968"></a><span class="lineno"> 968</span> <span class="preprocessor">#ifdef DEBUG_2D</span></div>
<div class="line"><a name="l00969"></a><span class="lineno"> 969</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"nachher\n"</span>;</div>
<div class="line"><a name="l00970"></a><span class="lineno"> 970</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0; p < peak_shapes.size(); ++p)</div>
<div class="line"><a name="l00971"></a><span class="lineno"> 971</span>  {</div>
<div class="line"><a name="l00972"></a><span class="lineno"> 972</span>  std::cout << peak_shapes[p].mz_position << <span class="stringliteral">"\t"</span> << peak_shapes[p].height</div>
<div class="line"><a name="l00973"></a><span class="lineno"> 973</span>  << <span class="stringliteral">"\t"</span> << peak_shapes[p].left_width << <span class="stringliteral">"\t"</span> << peak_shapes[p].right_width << std::endl;</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> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00976"></a><span class="lineno"> 976</span> <span class="preprocessor"></span> std::sort(peak_shapes.begin(), peak_shapes.end(), <a class="code" href="classOpenMS_1_1PeakShape_1_1PositionLess.html">PeakShape::PositionLess</a>());</div>
<div class="line"><a name="l00977"></a><span class="lineno"> 977</span>  pair.first = d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">iso_map_iter</a>->second.peaks.begin()->first + idx;</div>
<div class="line"><a name="l00978"></a><span class="lineno"> 978</span> </div>
<div class="line"><a name="l00979"></a><span class="lineno"> 979</span>  set_iter = lower_bound(d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">iso_map_iter</a>->second.peaks.begin(),</div>
<div class="line"><a name="l00980"></a><span class="lineno"> 980</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">iso_map_iter</a>->second.peaks.end(),</div>
<div class="line"><a name="l00981"></a><span class="lineno"> 981</span>  pair, <a class="code" href="structOpenMS_1_1PairComparatorFirstElement.html">PairComparatorFirstElement<IsotopeCluster::IndexPair></a>());</div>
<div class="line"><a name="l00982"></a><span class="lineno"> 982</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> p = 0;</div>
<div class="line"><a name="l00983"></a><span class="lineno"> 983</span>  <span class="keywordflow">while</span> (p < peak_shapes.size())</div>
<div class="line"><a name="l00984"></a><span class="lineno"> 984</span>  {</div>
<div class="line"><a name="l00985"></a><span class="lineno"> 985</span>  <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSSpectrum<></a>& spec = ms_exp[set_iter->first];</div>
<div class="line"><a name="l00986"></a><span class="lineno"> 986</span>  spec[set_iter->second].setMZ(peak_shapes[p].mz_position);</div>
<div class="line"><a name="l00987"></a><span class="lineno"> 987</span>  spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>()[3][set_iter->second] = peak_shapes[p].left_width;</div>
<div class="line"><a name="l00988"></a><span class="lineno"> 988</span>  spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>()[4][set_iter->second] = peak_shapes[p].right_width;</div>
<div class="line"><a name="l00989"></a><span class="lineno"> 989</span>  spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">getFloatDataArrays</a>()[1][set_iter->second] = peak_shapes[p].height; <span class="comment">// maximum intensity</span></div>
<div class="line"><a name="l00990"></a><span class="lineno"> 990</span>  <span class="comment">// calculate area</span></div>
<div class="line"><a name="l00991"></a><span class="lineno"> 991</span>  <span class="keywordflow">if</span> (peak_shapes[p].type == <a class="code" href="structOpenMS_1_1PeakShape.html#a1d1cfd8ffb84e947f82999c682b666a7a6ba0b50b9f0f84a5ad13827c57240f76">PeakShape::LORENTZ_PEAK</a>)</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>  <a class="code" href="structOpenMS_1_1PeakShape.html">PeakShape</a>& ps = peak_shapes[p];</div>
<div class="line"><a name="l00994"></a><span class="lineno"> 994</span>  <span class="keywordtype">double</span> x_left_endpoint = ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a0b633e3762805bc447c451f262a8f405">mz_position</a> - 1 / ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a6bd93679898a199380f450a9351fde28">left_width</a>* sqrt(ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a5343d7f469d61e6d3f4808a609094175">height</a> / 1 - 1);</div>
<div class="line"><a name="l00995"></a><span class="lineno"> 995</span>  <span class="keywordtype">double</span> x_rigth_endpoint = ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a0b633e3762805bc447c451f262a8f405">mz_position</a> + 1 / ps.<a class="code" href="structOpenMS_1_1PeakShape.html#aee68061fb00b7a84b354bac91e492039">right_width</a>* sqrt(ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a5343d7f469d61e6d3f4808a609094175">height</a> / 1 - 1);</div>
<div class="line"><a name="l00996"></a><span class="lineno"> 996</span>  <span class="keywordtype">double</span> area_left = -ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a5343d7f469d61e6d3f4808a609094175">height</a> / ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a6bd93679898a199380f450a9351fde28">left_width</a>* atan(ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a6bd93679898a199380f450a9351fde28">left_width</a> * (x_left_endpoint - ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a0b633e3762805bc447c451f262a8f405">mz_position</a>));</div>
<div class="line"><a name="l00997"></a><span class="lineno"> 997</span>  <span class="keywordtype">double</span> area_right = -ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a5343d7f469d61e6d3f4808a609094175">height</a> / ps.<a class="code" href="structOpenMS_1_1PeakShape.html#aee68061fb00b7a84b354bac91e492039">right_width</a>* atan(ps.<a class="code" href="structOpenMS_1_1PeakShape.html#aee68061fb00b7a84b354bac91e492039">right_width</a> * (ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a0b633e3762805bc447c451f262a8f405">mz_position</a> - x_rigth_endpoint));</div>
<div class="line"><a name="l00998"></a><span class="lineno"> 998</span>  spec[set_iter->second].setIntensity(area_left + area_right); <span class="comment">// area is stored as peak intensity</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>  <span class="keywordflow">else</span> <span class="comment">//It's a Sech - Peak</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>  <a class="code" href="structOpenMS_1_1PeakShape.html">PeakShape</a>& ps = peak_shapes[p];</div>
<div class="line"><a name="l01003"></a><span class="lineno"> 1003</span>  <span class="keywordtype">double</span> x_left_endpoint = ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a0b633e3762805bc447c451f262a8f405">mz_position</a> - 1 / ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a6bd93679898a199380f450a9351fde28">left_width</a>* boost::math::acosh(sqrt(ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a5343d7f469d61e6d3f4808a609094175">height</a> / 0.001));</div>
<div class="line"><a name="l01004"></a><span class="lineno"> 1004</span>  <span class="keywordtype">double</span> x_rigth_endpoint = ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a0b633e3762805bc447c451f262a8f405">mz_position</a> + 1 / ps.<a class="code" href="structOpenMS_1_1PeakShape.html#aee68061fb00b7a84b354bac91e492039">right_width</a>* boost::math::acosh(sqrt(ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a5343d7f469d61e6d3f4808a609094175">height</a> / 0.001));</div>
<div class="line"><a name="l01005"></a><span class="lineno"> 1005</span>  <span class="keywordtype">double</span> area_left = ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a5343d7f469d61e6d3f4808a609094175">height</a> / ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a6bd93679898a199380f450a9351fde28">left_width</a> * (sinh(ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a6bd93679898a199380f450a9351fde28">left_width</a> * (ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a0b633e3762805bc447c451f262a8f405">mz_position</a> - x_left_endpoint)) / cosh(ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a6bd93679898a199380f450a9351fde28">left_width</a> * (ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a0b633e3762805bc447c451f262a8f405">mz_position</a> - x_left_endpoint)));</div>
<div class="line"><a name="l01006"></a><span class="lineno"> 1006</span>  <span class="keywordtype">double</span> area_right = -ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a5343d7f469d61e6d3f4808a609094175">height</a> / ps.<a class="code" href="structOpenMS_1_1PeakShape.html#aee68061fb00b7a84b354bac91e492039">right_width</a> * (sinh(ps.<a class="code" href="structOpenMS_1_1PeakShape.html#aee68061fb00b7a84b354bac91e492039">right_width</a> * (ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a0b633e3762805bc447c451f262a8f405">mz_position</a> - x_rigth_endpoint)) / cosh(ps.<a class="code" href="structOpenMS_1_1PeakShape.html#aee68061fb00b7a84b354bac91e492039">right_width</a> * (ps.<a class="code" href="structOpenMS_1_1PeakShape.html#a0b633e3762805bc447c451f262a8f405">mz_position</a> - x_rigth_endpoint)));</div>
<div class="line"><a name="l01007"></a><span class="lineno"> 1007</span>  spec[set_iter->second].setIntensity(area_left + area_right); <span class="comment">// area is stored as peak intensity</span></div>
<div class="line"><a name="l01008"></a><span class="lineno"> 1008</span>  }</div>
<div class="line"><a name="l01009"></a><span class="lineno"> 1009</span>  ++set_iter;</div>
<div class="line"><a name="l01010"></a><span class="lineno"> 1010</span>  ++p;</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>  ++idx;</div>
<div class="line"><a name="l01013"></a><span class="lineno"> 1013</span>  peak_shapes.clear();</div>
<div class="line"><a name="l01014"></a><span class="lineno"> 1014</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>  ++counter;</div>
<div class="line"><a name="l01017"></a><span class="lineno"> 1017</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="keyword">template</span> <<span class="keyword">typename</span> InputSpectrumIterator, <span class="keyword">typename</span> OutputPeakType></div>
<div class="line"><a name="l01021"></a><span class="lineno"><a class="line" href="classOpenMS_1_1TwoDOptimization.html#a6d2b21b20b10f65e5a6052e8c8aa84e7"> 1021</a></span>  <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a6d2b21b20b10f65e5a6052e8c8aa84e7">TwoDOptimization::getRegionEndpoints_</a>(<a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<OutputPeakType></a>& exp,</div>
<div class="line"><a name="l01022"></a><span class="lineno"> 1022</span>  InputSpectrumIterator& first,</div>
<div class="line"><a name="l01023"></a><span class="lineno"> 1023</span>  InputSpectrumIterator& last,</div>
<div class="line"><a name="l01024"></a><span class="lineno"> 1024</span>  <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> iso_map_idx,</div>
<div class="line"><a name="l01025"></a><span class="lineno"> 1025</span>  <a class="code" href="classdouble.html">DoubleReal</a> noise_level,</div>
<div class="line"><a name="l01026"></a><span class="lineno"> 1026</span>  <a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html">TwoDOptimization::Data</a>& d)</div>
<div class="line"><a name="l01027"></a><span class="lineno"> 1027</span>  {</div>
<div class="line"><a name="l01028"></a><span class="lineno"> 1028</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>.clear();</div>
<div class="line"><a name="l01029"></a><span class="lineno"> 1029</span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> InputSpectrumIterator::value_type InputExperimentType;</div>
<div class="line"><a name="l01030"></a><span class="lineno"> 1030</span>  <span class="keyword">typedef</span> <span class="keyword">typename</span> InputExperimentType::value_type InputPeakType;</div>
<div class="line"><a name="l01031"></a><span class="lineno"> 1031</span>  <span class="keyword">typedef</span> std::multimap<DoubleReal, IsotopeCluster> MapType;</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>  <a class="code" href="classdouble.html">DoubleReal</a> rt, first_peak_mz, last_peak_mz;</div>
<div class="line"><a name="l01034"></a><span class="lineno"> 1034</span> </div>
<div class="line"><a name="l01035"></a><span class="lineno"> 1035</span>  <span class="comment">//MSSpectrum<InputPeakType> spec;</span></div>
<div class="line"><a name="l01036"></a><span class="lineno"> 1036</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSSpectrum.html">MSExperiment<InputPeakType>::SpectrumType</a> spec;</div>
<div class="line"><a name="l01037"></a><span class="lineno"> 1037</span>  InputPeakType peak;</div>
<div class="line"><a name="l01038"></a><span class="lineno"> 1038</span> </div>
<div class="line"><a name="l01039"></a><span class="lineno"> 1039</span>  MapType::iterator iso_map_iter = <a class="code" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a>.begin();</div>
<div class="line"><a name="l01040"></a><span class="lineno"> 1040</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < iso_map_idx; ++i)</div>
<div class="line"><a name="l01041"></a><span class="lineno"> 1041</span>  ++iso_map_iter;</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> <span class="preprocessor">#ifdef DEBUG2D</span></div>
<div class="line"><a name="l01044"></a><span class="lineno"> 1044</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"rt begin: "</span> << exp[iso_map_iter->second.scans[0]].getRT()</div>
<div class="line"><a name="l01045"></a><span class="lineno"> 1045</span>  << <span class="stringliteral">"\trt end: "</span> << exp[iso_map_iter->second.scans[iso_map_iter->second.scans.size() - 1]].getRT()</div>
<div class="line"><a name="l01046"></a><span class="lineno"> 1046</span>  << <span class="stringliteral">" \t"</span> << iso_map_iter->second.scans.<a class="code" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">size</a>() << <span class="stringliteral">" scans"</span></div>
<div class="line"><a name="l01047"></a><span class="lineno"> 1047</span>  << std::endl;</div>
<div class="line"><a name="l01048"></a><span class="lineno"> 1048</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l01049"></a><span class="lineno"> 1049</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l01050"></a><span class="lineno"> 1050</span>  <span class="comment">// get left and right endpoint for all scans in the current cluster</span></div>
<div class="line"><a name="l01051"></a><span class="lineno"> 1051</span>  <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i < iso_map_iter->second.scans.size(); ++i)</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>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html#a0bc3019d7d2ff6c73f261836bff0af3a">MSExperiment<OutputPeakType>::iterator</a> exp_it;</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>  <span class="comment">// first the right scan through binary search</span></div>
<div class="line"><a name="l01056"></a><span class="lineno"> 1056</span>  rt = exp[iso_map_iter->second.scans[i]].getRT();</div>
<div class="line"><a name="l01057"></a><span class="lineno"> 1057</span>  spec.<a class="code" href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">setRT</a>(rt);</div>
<div class="line"><a name="l01058"></a><span class="lineno"> 1058</span>  InputSpectrumIterator iter = lower_bound(first, last, spec, <span class="keyword">typename</span> <a class="code" href="structOpenMS_1_1MSSpectrum_1_1RTLess.html">MSSpectrum<InputPeakType>::RTLess</a>());</div>
<div class="line"><a name="l01059"></a><span class="lineno"> 1059</span>  <span class="comment">// if(iter->getRT() != rt) --iter;</span></div>
<div class="line"><a name="l01060"></a><span class="lineno"> 1060</span>  exp_it = exp.<a class="code" href="classOpenMS_1_1MSExperiment.html#adb2f0f3e10754ca4dc7be677f15689a3">RTBegin</a>(rt);</div>
<div class="line"><a name="l01061"></a><span class="lineno"> 1061</span> <span class="preprocessor">#ifdef DEBUG2D</span></div>
<div class="line"><a name="l01062"></a><span class="lineno"> 1062</span> <span class="preprocessor"></span> std::cout << exp_it->getRT() << <span class="stringliteral">" vs "</span> << iter->getRT() << std::endl;</div>
<div class="line"><a name="l01063"></a><span class="lineno"> 1063</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l01064"></a><span class="lineno"> 1064</span> <span class="preprocessor"></span> <span class="comment">// now the right mz</span></div>
<div class="line"><a name="l01065"></a><span class="lineno"> 1065</span>  <a class="code" href="structOpenMS_1_1IsotopeCluster.html#a0cab124671a3ada269f0553e1c8934da">IsotopeCluster::IndexPair</a> pair;</div>
<div class="line"><a name="l01066"></a><span class="lineno"> 1066</span>  pair.first = iso_map_iter->second.peaks.<a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>()->first + i;</div>
<div class="line"><a name="l01067"></a><span class="lineno"> 1067</span>  <span class="comment">// get iterator in peaks-set that points to the first peak in the current scan</span></div>
<div class="line"><a name="l01068"></a><span class="lineno"> 1068</span>  IsotopeCluster::IndexSet::const_iterator set_iter = lower_bound(iso_map_iter->second.peaks.begin(),</div>
<div class="line"><a name="l01069"></a><span class="lineno"> 1069</span>  iso_map_iter->second.peaks.end(),</div>
<div class="line"><a name="l01070"></a><span class="lineno"> 1070</span>  pair, <a class="code" href="structOpenMS_1_1PairComparatorFirstElement.html">PairComparatorFirstElement<IsotopeCluster::IndexPair></a>());</div>
<div class="line"><a name="l01071"></a><span class="lineno"> 1071</span> </div>
<div class="line"><a name="l01072"></a><span class="lineno"> 1072</span>  <span class="comment">// consider a bit more of the signal to the left</span></div>
<div class="line"><a name="l01073"></a><span class="lineno"> 1073</span>  first_peak_mz = (exp_it-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>() + set_iter->second)->getMZ() - 1;</div>
<div class="line"><a name="l01074"></a><span class="lineno"> 1074</span> </div>
<div class="line"><a name="l01075"></a><span class="lineno"> 1075</span>  <span class="comment">// find the last entry with this rt-value</span></div>
<div class="line"><a name="l01076"></a><span class="lineno"> 1076</span>  ++pair.first;</div>
<div class="line"><a name="l01077"></a><span class="lineno"> 1077</span>  IsotopeCluster::IndexSet::const_iterator set_iter2 = lower_bound(iso_map_iter->second.peaks.begin(),</div>
<div class="line"><a name="l01078"></a><span class="lineno"> 1078</span>  iso_map_iter->second.peaks.end(),</div>
<div class="line"><a name="l01079"></a><span class="lineno"> 1079</span>  pair, <a class="code" href="structOpenMS_1_1PairComparatorFirstElement.html">PairComparatorFirstElement<IsotopeCluster::IndexPair></a>());</div>
<div class="line"><a name="l01080"></a><span class="lineno"> 1080</span> </div>
<div class="line"><a name="l01081"></a><span class="lineno"> 1081</span>  <span class="keywordflow">if</span> (i == iso_map_iter->second.scans.size() - 1)</div>
<div class="line"><a name="l01082"></a><span class="lineno"> 1082</span>  {</div>
<div class="line"><a name="l01083"></a><span class="lineno"> 1083</span>  set_iter2 = iso_map_iter->second.peaks.end();</div>
<div class="line"><a name="l01084"></a><span class="lineno"> 1084</span>  --set_iter2;</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">else</span> <span class="keywordflow">if</span> (set_iter2 != iso_map_iter->second.peaks.begin())</div>
<div class="line"><a name="l01087"></a><span class="lineno"> 1087</span>  --set_iter2;</div>
<div class="line"><a name="l01088"></a><span class="lineno"> 1088</span> </div>
<div class="line"><a name="l01089"></a><span class="lineno"> 1089</span>  last_peak_mz = (exp_it-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>() + set_iter2->second)->getMZ() + 1;</div>
<div class="line"><a name="l01090"></a><span class="lineno"> 1090</span> </div>
<div class="line"><a name="l01091"></a><span class="lineno"> 1091</span>  <span class="comment">//std::cout << rt<<": first peak mz "<<first_peak_mz << "\tlast peak mz "<<last_peak_mz <<std::endl;</span></div>
<div class="line"><a name="l01092"></a><span class="lineno"> 1092</span>  peak.setPosition(first_peak_mz);</div>
<div class="line"><a name="l01093"></a><span class="lineno"> 1093</span>  <span class="keyword">typename</span> <a class="code" href="classOpenMS_1_1MSExperiment.html">MSExperiment<InputPeakType>::SpectrumType::const_iterator</a> raw_data_iter</div>
<div class="line"><a name="l01094"></a><span class="lineno"> 1094</span>  = lower_bound(iter->begin(), iter->end(), peak, <span class="keyword">typename</span> InputPeakType::PositionLess());</div>
<div class="line"><a name="l01095"></a><span class="lineno"> 1095</span>  <span class="keywordflow">if</span> (raw_data_iter != iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>())</div>
<div class="line"><a name="l01096"></a><span class="lineno"> 1096</span>  {</div>
<div class="line"><a name="l01097"></a><span class="lineno"> 1097</span>  --raw_data_iter;</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>  <a class="code" href="classdouble.html">DoubleReal</a> intensity = raw_data_iter->getIntensity();</div>
<div class="line"><a name="l01100"></a><span class="lineno"> 1100</span>  <span class="comment">// while the intensity is falling go to the left</span></div>
<div class="line"><a name="l01101"></a><span class="lineno"> 1101</span>  <span class="keywordflow">while</span> (raw_data_iter != iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>() && (raw_data_iter - 1)->getIntensity() < intensity &&</div>
<div class="line"><a name="l01102"></a><span class="lineno"> 1102</span>  (raw_data_iter - 1)->getIntensity() > noise_level)</div>
<div class="line"><a name="l01103"></a><span class="lineno"> 1103</span>  {</div>
<div class="line"><a name="l01104"></a><span class="lineno"> 1104</span>  --raw_data_iter;</div>
<div class="line"><a name="l01105"></a><span class="lineno"> 1105</span>  intensity = raw_data_iter->getIntensity();</div>
<div class="line"><a name="l01106"></a><span class="lineno"> 1106</span>  }</div>
<div class="line"><a name="l01107"></a><span class="lineno"> 1107</span>  ++raw_data_iter;</div>
<div class="line"><a name="l01108"></a><span class="lineno"> 1108</span>  <a class="code" href="structOpenMS_1_1IsotopeCluster.html#a0cab124671a3ada269f0553e1c8934da">IsotopeCluster::IndexPair</a> left, right;</div>
<div class="line"><a name="l01109"></a><span class="lineno"> 1109</span>  left.first = distance(first, iter);</div>
<div class="line"><a name="l01110"></a><span class="lineno"> 1110</span>  left.second = raw_data_iter - iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>();</div>
<div class="line"><a name="l01111"></a><span class="lineno"> 1111</span> <span class="preprocessor">#ifdef DEBUG2D</span></div>
<div class="line"><a name="l01112"></a><span class="lineno"> 1112</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"left: "</span> << iter->getRT() << <span class="stringliteral">"\t"</span> << raw_data_iter->getMZ() << std::endl;</div>
<div class="line"><a name="l01113"></a><span class="lineno"> 1113</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l01114"></a><span class="lineno"> 1114</span> <span class="preprocessor"></span> <span class="comment">// consider a bit more of the signal to the right</span></div>
<div class="line"><a name="l01115"></a><span class="lineno"> 1115</span>  peak.setPosition(last_peak_mz + 1);</div>
<div class="line"><a name="l01116"></a><span class="lineno"> 1116</span>  raw_data_iter</div>
<div class="line"><a name="l01117"></a><span class="lineno"> 1117</span>  = upper_bound(iter->begin(), iter->end(), peak, <span class="keyword">typename</span> InputPeakType::PositionLess());</div>
<div class="line"><a name="l01118"></a><span class="lineno"> 1118</span>  <span class="keywordflow">if</span> (raw_data_iter == iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">end</a>())</div>
<div class="line"><a name="l01119"></a><span class="lineno"> 1119</span>  --raw_data_iter;</div>
<div class="line"><a name="l01120"></a><span class="lineno"> 1120</span>  intensity = raw_data_iter->getIntensity();</div>
<div class="line"><a name="l01121"></a><span class="lineno"> 1121</span>  <span class="comment">// while the intensity is falling go to the right</span></div>
<div class="line"><a name="l01122"></a><span class="lineno"> 1122</span>  <span class="keywordflow">while</span> (raw_data_iter + 1 != iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">end</a>() && (raw_data_iter + 1)->getIntensity() < intensity)</div>
<div class="line"><a name="l01123"></a><span class="lineno"> 1123</span>  {</div>
<div class="line"><a name="l01124"></a><span class="lineno"> 1124</span>  ++raw_data_iter;</div>
<div class="line"><a name="l01125"></a><span class="lineno"> 1125</span>  intensity = raw_data_iter->getIntensity();</div>
<div class="line"><a name="l01126"></a><span class="lineno"> 1126</span>  <span class="keywordflow">if</span> ((raw_data_iter + 1 != iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">end</a>()) && (raw_data_iter + 1)->getIntensity() > noise_level)</div>
<div class="line"><a name="l01127"></a><span class="lineno"> 1127</span>  <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l01128"></a><span class="lineno"> 1128</span>  }</div>
<div class="line"><a name="l01129"></a><span class="lineno"> 1129</span>  right.first = left.first;</div>
<div class="line"><a name="l01130"></a><span class="lineno"> 1130</span>  right.second = raw_data_iter - iter-><a class="code" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">begin</a>();</div>
<div class="line"><a name="l01131"></a><span class="lineno"> 1131</span> <span class="preprocessor">#ifdef DEBUG2D</span></div>
<div class="line"><a name="l01132"></a><span class="lineno"> 1132</span> <span class="preprocessor"></span> std::cout << <span class="stringliteral">"right: "</span> << iter->getRT() << <span class="stringliteral">"\t"</span> << raw_data_iter->getMZ() << std::endl;</div>
<div class="line"><a name="l01133"></a><span class="lineno"> 1133</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l01134"></a><span class="lineno"> 1134</span> <span class="preprocessor"></span> <span class="comment">// region endpoints are stored in global vector</span></div>
<div class="line"><a name="l01135"></a><span class="lineno"> 1135</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>.push_back(left);</div>
<div class="line"><a name="l01136"></a><span class="lineno"> 1136</span>  d.<a class="code" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">signal2D</a>.push_back(right);</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="preprocessor">#ifdef DEBUG2D</span></div>
<div class="line"><a name="l01139"></a><span class="lineno"> 1139</span> <span class="preprocessor"></span> <span class="comment">//std::cout << "fertig"<< std::endl;</span></div>
<div class="line"><a name="l01140"></a><span class="lineno"> 1140</span>  std::cout << first_peak_mz << <span class="stringliteral">"\t"</span> << last_peak_mz << std::endl;</div>
<div class="line"><a name="l01141"></a><span class="lineno"> 1141</span> <span class="preprocessor">#endif</span></div>
<div class="line"><a name="l01142"></a><span class="lineno"> 1142</span> <span class="preprocessor"></span> }</div>
<div class="line"><a name="l01143"></a><span class="lineno"> 1143</span> </div>
<div class="line"><a name="l01144"></a><span class="lineno"> 1144</span> }</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="preprocessor">#endif //OPENMS_TRANSFORMATIONS_RAW2PEAK_TWODOPTIMIZATION_H</span></div>
<div class="ttc" id="structOpenMS_1_1OptimizePick_1_1Data_html_a649cc300c964845ccc272fd2229b6ed4"><div class="ttname"><a href="structOpenMS_1_1OptimizePick_1_1Data.html#a649cc300c964845ccc272fd2229b6ed4">OpenMS::OptimizePick::Data::positions</a></div><div class="ttdeci">std::vector< double > positions</div><div class="ttdoc">Positions and intensity values of the raw data. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:123</div></div>
<div class="ttc" id="namespaceOpenMS_1_1Constants_html_a93a8dc068053ec44ee7e45864ef969f7"><div class="ttname"><a href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a></div><div class="ttdeci">const double k</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="structOpenMS_1_1PeakShape_html"><div class="ttname"><a href="structOpenMS_1_1PeakShape.html">OpenMS::PeakShape</a></div><div class="ttdoc">Internal representation of a peak shape (used by the PeakPickerCWT) </div><div class="ttdef"><b>Definition:</b> PeakShape.h:51</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a6d2b21b20b10f65e5a6052e8c8aa84e7"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a6d2b21b20b10f65e5a6052e8c8aa84e7">OpenMS::TwoDOptimization::getRegionEndpoints_</a></div><div class="ttdeci">void getRegionEndpoints_(MSExperiment< OutputPeakType > &exp, InputSpectrumIterator &first, InputSpectrumIterator &last, Size iso_map_idx, DoubleReal noise_level, TwoDOptimization::Data &d)</div><div class="ttdoc">Get the indices of the first and last raw data point of this region. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:1021</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizePick_1_1Data_html"><div class="ttname"><a href="structOpenMS_1_1OptimizePick_1_1Data.html">OpenMS::OptimizePick::Data</a></div><div class="ttdef"><b>Definition:</b> OptimizePick.h:120</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a50d07207174c609658e117b2aa89cb10"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a50d07207174c609658e117b2aa89cb10">OpenMS::TwoDOptimization::matching_peaks_</a></div><div class="ttdeci">std::map< Int, std::vector< PeakIndex > > matching_peaks_</div><div class="ttdoc">Indices of peaks in the adjacent scans matching peaks in the scan with no. ref_scan. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:212</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a9d78a687cf2a391198bb3cbc08bc06cb"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">OpenMS::MSExperiment::size</a></div><div class="ttdeci">Size size() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:117</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_aef02420ae0f171972e40c069ec5931be"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#aef02420ae0f171972e40c069ec5931be">OpenMS::TwoDOptimization::setMZTolerance</a></div><div class="ttdeci">void setMZTolerance(DoubleReal tolerance_mz)</div><div class="ttdoc">Mutable access to the matching epsilon. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:107</div></div>
<div class="ttc" id="structOpenMS_1_1IsotopeCluster_html_a0cab124671a3ada269f0553e1c8934da"><div class="ttname"><a href="structOpenMS_1_1IsotopeCluster.html#a0cab124671a3ada269f0553e1c8934da">OpenMS::IsotopeCluster::IndexPair</a></div><div class="ttdeci">std::pair< Size, Size > IndexPair</div><div class="ttdoc">An index e.g. in an MSExperiment. </div><div class="ttdef"><b>Definition:</b> IsotopeCluster.h:48</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a3049e1d8765313f967f17885188d767c"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a3049e1d8765313f967f17885188d767c">OpenMS::MSExperiment::Iterator</a></div><div class="ttdeci">std::vector< SpectrumType >::iterator Iterator</div><div class="ttdoc">Mutable iterator. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:101</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_aacb90f036a8fff25704290ac0c34364c"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#aacb90f036a8fff25704290ac0c34364c">OpenMS::TwoDOptimization::getPenalties</a></div><div class="ttdeci">const OptimizationFunctions::PenaltyFactorsIntensity & getPenalties() const </div><div class="ttdoc">Non-mutable access to the minimal number of adjacent scans. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:150</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_aafe5d0ee09d7e6ee8a5f12b9f5f40a19"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#aafe5d0ee09d7e6ee8a5f12b9f5f40a19">OpenMS::TwoDOptimization::getMZTolerance</a></div><div class="ttdeci">DoubleReal getMZTolerance() const </div><div class="ttdoc">Non-mutable access to the matching epsilon. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:105</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html_a28c73e623c63a4fe3bfceb1ae8274f39"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">OpenMS::DefaultParamHandler::param_</a></div><div class="ttdeci">Param param_</div><div class="ttdoc">Container for current parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:148</div></div>
<div class="ttc" id="classOpenMS_1_1PeakShape_1_1PositionLess_html"><div class="ttname"><a href="classOpenMS_1_1PeakShape_1_1PositionLess.html">OpenMS::PeakShape::PositionLess</a></div><div class="ttdoc">Comparison of mz_positions. </div><div class="ttdef"><b>Definition:</b> PeakShape.h:154</div></div>
<div class="ttc" id="structOpenMS_1_1PeakShape_html_a5343d7f469d61e6d3f4808a609094175"><div class="ttname"><a href="structOpenMS_1_1PeakShape.html#a5343d7f469d61e6d3f4808a609094175">OpenMS::PeakShape::height</a></div><div class="ttdeci">DoubleReal height</div><div class="ttdoc">Maximum intensity of the peak shape. </div><div class="ttdef"><b>Definition:</b> PeakShape.h:131</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a0409337ea8ad2ae8fde8f6cba1e889a2"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a0409337ea8ad2ae8fde8f6cba1e889a2">OpenMS::TwoDOptimization::eps_rel_</a></div><div class="ttdeci">DoubleReal eps_rel_</div><div class="ttdoc">Convergence Parameter: Maximal relative error. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:219</div></div>
<div class="ttc" id="structOpenMS_1_1MSSpectrum_1_1RTLess_html"><div class="ttname"><a href="structOpenMS_1_1MSSpectrum_1_1RTLess.html">OpenMS::MSSpectrum::RTLess</a></div><div class="ttdoc">Comparator for the retention time. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:94</div></div>
<div class="ttc" id="group__Concept_html_gaba0996d26f7be2572973245b51852757"><div class="ttname"><a href="group__Concept.html#gaba0996d26f7be2572973245b51852757">OpenMS::UInt</a></div><div class="ttdeci">unsigned int UInt</div><div class="ttdoc">Unsigned integer type. </div><div class="ttdef"><b>Definition:</b> Types.h:92</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_aa82b642dc0b200f292a5f44e6458bf16"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#aa82b642dc0b200f292a5f44e6458bf16">OpenMS::TwoDOptimization::residual2D_</a></div><div class="ttdeci">static Int residual2D_(const gsl_vector *x, void *params, gsl_vector *f)</div><div class="ttdoc">Function computing estimated signal and its deviation to the experimental signal*/. </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="structOpenMS_1_1TwoDOptimization_1_1Data_html"><div class="ttname"><a href="structOpenMS_1_1TwoDOptimization_1_1Data.html">OpenMS::TwoDOptimization::Data</a></div><div class="ttdoc">Helper struct (contains the size of an area and a raw data container) </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:185</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a74f373ec1e1e803064c86d9b0f18abdd"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a74f373ec1e1e803064c86d9b0f18abdd">OpenMS::TwoDOptimization::searchInScan_</a></div><div class="ttdeci">std::vector< DoubleReal >::iterator searchInScan_(std::vector< DoubleReal >::iterator scan_begin, std::vector< DoubleReal >::iterator scan_end, DoubleReal current_mz)</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a2387033802383edbdc95f9bbb12a707e"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">OpenMS::MSExperiment::begin</a></div><div class="ttdeci">Iterator begin()</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:147</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_1TwoDOptimization_html_ae71d03ba24d6ab714f95b65a524b9ec4"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#ae71d03ba24d6ab714f95b65a524b9ec4">OpenMS::TwoDOptimization::~TwoDOptimization</a></div><div class="ttdeci">virtual ~TwoDOptimization()</div><div class="ttdoc">Destructor. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:98</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a0c0b2f69c6c06fae06bd27ff373b07f0"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">OpenMS::TwoDOptimization::iso_map_</a></div><div class="ttdeci">std::multimap< DoubleReal, IsotopeCluster > iso_map_</div><div class="ttdoc">stores the retention time of each isotopic cluster </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:199</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="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors_html_abb10592f0ea83f824c0a14f4afa95be4"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#abb10592f0ea83f824c0a14f4afa95be4">OpenMS::OptimizationFunctions::PenaltyFactors::lWidth</a></div><div class="ttdeci">double lWidth</div><div class="ttdoc">Penalty factor for the peak shape&#39;s left width parameter. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:91</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_acbc4c0b42c88614c321ed3a8e4075c08"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#acbc4c0b42c88614c321ed3a8e4075c08">OpenMS::TwoDOptimization::tolerance_mz_</a></div><div class="ttdeci">DoubleReal tolerance_mz_</div><div class="ttdoc">threshold for the difference in the peak position of two matching peaks </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:208</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a6ed5164a8b4af4b3de8e04912350acfb"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a6ed5164a8b4af4b3de8e04912350acfb">OpenMS::TwoDOptimization::setMaxRelError</a></div><div class="ttdeci">void setMaxRelError(DoubleReal eps_rel)</div><div class="ttdoc">Mutable access to the maximal relative error. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:134</div></div>
<div class="ttc" id="classOpenMS_1_1DataValue_html"><div class="ttname"><a href="classOpenMS_1_1DataValue.html">OpenMS::DataValue</a></div><div class="ttdoc">Class to hold strings, numeric values, lists of strings and lists of numeric values. </div><div class="ttdef"><b>Definition:</b> DataValue.h:57</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a17e2d6f48048565ca00dee8f87da38ba"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">OpenMS::TwoDOptimization::optimizeRegions_</a></div><div class="ttdeci">void optimizeRegions_(InputSpectrumIterator &first, InputSpectrumIterator &last, MSExperiment< OutputPeakType > &ms_exp)</div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:584</div></div>
<div class="ttc" id="structOpenMS_1_1TwoDOptimization_1_1Data_html_ad777935432d69859f870fd8cc1af7638"><div class="ttname"><a href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">OpenMS::TwoDOptimization::Data::iso_map_iter</a></div><div class="ttdeci">std::multimap< DoubleReal, IsotopeCluster >::iterator iso_map_iter</div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:188</div></div>
<div class="ttc" id="structOpenMS_1_1TwoDOptimization_1_1Data_html_a4dbfc949c1c63f8a02dafd6a592d7955"><div class="ttname"><a href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a4dbfc949c1c63f8a02dafd6a592d7955">OpenMS::TwoDOptimization::Data::penalties</a></div><div class="ttdeci">OptimizationFunctions::PenaltyFactorsIntensity penalties</div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:193</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a1ba9944277216253f5225aa74581147e"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a1ba9944277216253f5225aa74581147e">OpenMS::TwoDOptimization::eps_abs_</a></div><div class="ttdeci">DoubleReal eps_abs_</div><div class="ttdoc">Convergence Parameter: Maximal absolute error. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:216</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_add19caffdc34d20e18e084922846ec3a"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#add19caffdc34d20e18e084922846ec3a">OpenMS::TwoDOptimization::getMaxPeakDistance</a></div><div class="ttdeci">DoubleReal getMaxPeakDistance() const </div><div class="ttdoc">Non-mutable access to the maximal peak distance in a cluster. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_ab45dae688fc5d8983727abffa4389003"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">OpenMS::MSExperiment::end</a></div><div class="ttdeci">Iterator end()</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:157</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_ac061845432fbff0f67d3212a815ebac9"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#ac061845432fbff0f67d3212a815ebac9">OpenMS::TwoDOptimization::getMaxRelError</a></div><div class="ttdeci">DoubleReal getMaxRelError() const </div><div class="ttdoc">Non-mutable access to the maximal relative error. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:132</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_adb2f0f3e10754ca4dc7be677f15689a3"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#adb2f0f3e10754ca4dc7be677f15689a3">OpenMS::MSExperiment::RTBegin</a></div><div class="ttdeci">ConstIterator RTBegin(CoordinateType rt) const </div><div class="ttdoc">Fast search for spectrum range begin. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:349</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a850156405bdec2d3a4761d49310151e7"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a850156405bdec2d3a4761d49310151e7">OpenMS::TwoDOptimization::setMaxAbsError</a></div><div class="ttdeci">void setMaxAbsError(DoubleReal eps_abs)</div><div class="ttdoc">Mutable access to the maximal absolute error. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:125</div></div>
<div class="ttc" id="MSSpectrum_8h_html"><div class="ttname"><a href="MSSpectrum_8h.html">MSSpectrum.h</a></div></div>
<div class="ttc" id="PeakIndex_8h_html"><div class="ttname"><a href="PeakIndex_8h.html">PeakIndex.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html_a0bc3019d7d2ff6c73f261836bff0af3a"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#a0bc3019d7d2ff6c73f261836bff0af3a">OpenMS::MSExperiment::iterator</a></div><div class="ttdeci">Base::iterator iterator</div><div class="ttdef"><b>Definition:</b> MSExperiment.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a8e4d88640e61ef82005212a8583ba784"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a8e4d88640e61ef82005212a8583ba784">OpenMS::TwoDOptimization::findMatchingPeaks_</a></div><div class="ttdeci">void findMatchingPeaks_(std::multimap< DoubleReal, IsotopeCluster >::iterator &it, MSExperiment<> &ms_exp)</div><div class="ttdoc">Identify matching peak in a peak cluster. </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_1MSSpectrum_html"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html">OpenMS::MSSpectrum< PeakType ></a></div></div>
<div class="ttc" id="PeakShape_8h_html"><div class="ttname"><a href="PeakShape_8h.html">PeakShape.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_ab25862b6e7eaee9e6739c52ae57d0896"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#ab25862b6e7eaee9e6739c52ae57d0896">OpenMS::TwoDOptimization::jacobian2D_</a></div><div class="ttdeci">static Int jacobian2D_(const gsl_vector *x, void *params, gsl_matrix *J)</div><div class="ttdoc">Function computing the Jacobian */. </div></div>
<div class="ttc" id="structOpenMS_1_1PeakShape_html_a1d1cfd8ffb84e947f82999c682b666a7"><div class="ttname"><a href="structOpenMS_1_1PeakShape.html#a1d1cfd8ffb84e947f82999c682b666a7">OpenMS::PeakShape::Type</a></div><div class="ttdeci">Type</div><div class="ttdoc">Peak shape type (asymmetric lorentzian or asymmetric hyperbolic secans squared). </div><div class="ttdef"><b>Definition:</b> PeakShape.h:68</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a165bfd792d0e5b693e0cdd6a9782d27f"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a165bfd792d0e5b693e0cdd6a9782d27f">OpenMS::TwoDOptimization::setPenalties</a></div><div class="ttdeci">void setPenalties(OptimizationFunctions::PenaltyFactorsIntensity &penalties)</div><div class="ttdoc">Mutable access to the minimal number of adjacent scans. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:152</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1IllegalArgument_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1IllegalArgument.html">OpenMS::Exception::IllegalArgument</a></div><div class="ttdoc">A method or algorithm argument contains illegal values. </div><div class="ttdef"><b>Definition:</b> Exception.h:634</div></div>
<div class="ttc" id="structOpenMS_1_1IsotopeCluster_html_ad4c8689a4cd1334e0eccdadcb0cc5a54"><div class="ttname"><a href="structOpenMS_1_1IsotopeCluster.html#ad4c8689a4cd1334e0eccdadcb0cc5a54">OpenMS::IsotopeCluster::peaks</a></div><div class="ttdeci">ChargedIndexSet peaks</div><div class="ttdoc">peaks in this cluster </div><div class="ttdef"><b>Definition:</b> IsotopeCluster.h:72</div></div>
<div class="ttc" id="classOpenMS_1_1Param_html_abd0f5571675ec99e1aa647b39e2a8711"><div class="ttname"><a href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">OpenMS::Param::getValue</a></div><div class="ttdeci">const DataValue & getValue(const String &key) const </div><div class="ttdoc">Returns a value of a parameter. </div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html_ae69ba4a78f94acc6d88ec067397bf490"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html#ae69ba4a78f94acc6d88ec067397bf490">OpenMS::OptimizePick::optimize</a></div><div class="ttdeci">void optimize(std::vector< PeakShape > &peaks, Data &data)</div><div class="ttdoc">Start the optimization of the peak shapes peaks. The original peak shapes will be subsituted by the o...</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a5ecbb7085dd05993affbe76a8eae8718"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a5ecbb7085dd05993affbe76a8eae8718">OpenMS::TwoDOptimization::real_2D_</a></div><div class="ttdeci">bool real_2D_</div><div class="ttdoc">Optimization considering all scans of a cluster or optimization of each scan separately. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:225</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a58b5225db8586aea7dd011a7447de6af"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a58b5225db8586aea7dd011a7447de6af">OpenMS::TwoDOptimization::max_peak_distance_</a></div><div class="ttdeci">DoubleReal max_peak_distance_</div><div class="ttdoc">upper bound for distance between two peaks belonging to the same region </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:205</div></div>
<div class="ttc" id="structOpenMS_1_1PeakShape_html_a1d1cfd8ffb84e947f82999c682b666a7a6ba0b50b9f0f84a5ad13827c57240f76"><div class="ttname"><a href="structOpenMS_1_1PeakShape.html#a1d1cfd8ffb84e947f82999c682b666a7a6ba0b50b9f0f84a5ad13827c57240f76">OpenMS::PeakShape::LORENTZ_PEAK</a></div><div class="ttdef"><b>Definition:</b> PeakShape.h:70</div></div>
<div class="ttc" id="structOpenMS_1_1TwoDOptimization_1_1Data_html_a9d5caa74a619fd37c7352fce078259fd"><div class="ttname"><a href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a9d5caa74a619fd37c7352fce078259fd">OpenMS::TwoDOptimization::Data::total_nr_peaks</a></div><div class="ttdeci">Size total_nr_peaks</div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:189</div></div>
<div class="ttc" id="structOpenMS_1_1TwoDOptimization_1_1Data_html_a34171d03bcd36d5482f4c90b6e7c0d45"><div class="ttname"><a href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a34171d03bcd36d5482f4c90b6e7c0d45">OpenMS::TwoDOptimization::Data::signal</a></div><div class="ttdeci">std::vector< DoubleReal > signal</div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:195</div></div>
<div class="ttc" id="IsotopeCluster_8h_html"><div class="ttname"><a href="IsotopeCluster_8h.html">IsotopeCluster.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_afe966e2a453a2c21000f38f431bc6205"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#afe966e2a453a2c21000f38f431bc6205">OpenMS::TwoDOptimization::setMaxPeakDistance</a></div><div class="ttdeci">void setMaxPeakDistance(DoubleReal max_peak_distance)</div><div class="ttdoc">Mutable access to the maximal peak distance in a cluster. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:116</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a1491750eda19a5fae8d6aa0deafb60ce"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a1491750eda19a5fae8d6aa0deafb60ce">OpenMS::TwoDOptimization::penalties_</a></div><div class="ttdeci">OptimizationFunctions::PenaltyFactorsIntensity penalties_</div><div class="ttdoc">Penalty factors for some parameters in the optimization. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:229</div></div>
<div class="ttc" id="structOpenMS_1_1TwoDOptimization_1_1Data_html_a0aa2a591a3184b849b2dceb401790f2c"><div class="ttname"><a href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">OpenMS::TwoDOptimization::Data::signal2D</a></div><div class="ttdeci">std::vector< std::pair< SignedSize, SignedSize > > signal2D</div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:187</div></div>
<div class="ttc" id="structOpenMS_1_1PeakShape_html_aee68061fb00b7a84b354bac91e492039"><div class="ttname"><a href="structOpenMS_1_1PeakShape.html#aee68061fb00b7a84b354bac91e492039">OpenMS::PeakShape::right_width</a></div><div class="ttdeci">DoubleReal right_width</div><div class="ttdoc">Right width parameter. </div><div class="ttdef"><b>Definition:</b> PeakShape.h:137</div></div>
<div class="ttc" id="structOpenMS_1_1TwoDOptimization_1_1Data_html_a5e129442f31432fc1dbb5d3573754012"><div class="ttname"><a href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a5e129442f31432fc1dbb5d3573754012">OpenMS::TwoDOptimization::Data::positions</a></div><div class="ttdeci">std::vector< DoubleReal > positions</div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:194</div></div>
<div class="ttc" id="OptimizePeakDeconvolution_8h_html"><div class="ttname"><a href="OptimizePeakDeconvolution_8h.html">OptimizePeakDeconvolution.h</a></div></div>
<div class="ttc" id="structOpenMS_1_1TwoDOptimization_1_1Data_html_a16930394d61d06ff8227219211874592"><div class="ttname"><a href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a16930394d61d06ff8227219211874592">OpenMS::TwoDOptimization::Data::raw_data_first</a></div><div class="ttdeci">MSExperiment< Peak1D >::ConstIterator raw_data_first</div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:192</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors_html_a5e9dd75fc35bca3ebe4981821077aebe"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a5e9dd75fc35bca3ebe4981821077aebe">OpenMS::OptimizationFunctions::PenaltyFactors::pos</a></div><div class="ttdeci">double pos</div><div class="ttdoc">Penalty factor for the peak shape&#39;s position. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:89</div></div>
<div class="ttc" id="classOpenMS_1_1MSExperiment_html"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html">OpenMS::MSExperiment</a></div><div class="ttdoc">Representation of a mass spectrometry experiment. </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:68</div></div>
<div class="ttc" id="OptimizePick_8h_html"><div class="ttname"><a href="OptimizePick_8h.html">OptimizePick.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_af0c0642cd0366fd192034cf58036fb11"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#af0c0642cd0366fd192034cf58036fb11">OpenMS::TwoDOptimization::curr_region_</a></div><div class="ttdeci">std::multimap< DoubleReal, IsotopeCluster >::const_iterator curr_region_</div><div class="ttdoc">Pointer to the current region. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:202</div></div>
<div class="ttc" id="structOpenMS_1_1TwoDOptimization_1_1Data_html_a2dcab4dd664c2b08f478ebde32edaa74"><div class="ttname"><a href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a2dcab4dd664c2b08f478ebde32edaa74">OpenMS::TwoDOptimization::Data::picked_peaks</a></div><div class="ttdeci">MSExperiment picked_peaks</div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:191</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors_html_a478a632c0b5a363e215061428eee1a1c"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a478a632c0b5a363e215061428eee1a1c">OpenMS::OptimizationFunctions::PenaltyFactors::rWidth</a></div><div class="ttdeci">double rWidth</div><div class="ttdoc">Penalty factor for the peak shape&#39;s right width parameter. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:93</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_aac8c50f318154e9e5b7b01aee806e17f"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">OpenMS::MSSpectrum::setRT</a></div><div class="ttdeci">void setRT(DoubleReal rt)</div><div class="ttdoc">Sets the absolute retention time (is seconds) </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:221</div></div>
<div class="ttc" id="structOpenMS_1_1IsotopeCluster_html_a47b3744693f84a7d94f7181676f36758"><div class="ttname"><a href="structOpenMS_1_1IsotopeCluster.html#a47b3744693f84a7d94f7181676f36758">OpenMS::IsotopeCluster::scans</a></div><div class="ttdeci">std::vector< Size > scans</div><div class="ttdoc">the scans of this cluster </div><div class="ttdef"><b>Definition:</b> IsotopeCluster.h:75</div></div>
<div class="ttc" id="structOpenMS_1_1PeakShape_html_a6bd93679898a199380f450a9351fde28"><div class="ttname"><a href="structOpenMS_1_1PeakShape.html#a6bd93679898a199380f450a9351fde28">OpenMS::PeakShape::left_width</a></div><div class="ttdeci">DoubleReal left_width</div><div class="ttdoc">Left width parameter. </div><div class="ttdef"><b>Definition:</b> PeakShape.h:135</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_1MSExperiment_html_ac6e61de369e994009e36f344f99c15ad"><div class="ttname"><a href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">OpenMS::MSExperiment::empty</a></div><div class="ttdeci">bool empty() const </div><div class="ttdef"><b>Definition:</b> MSExperiment.h:127</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_ae11715606af5b9d6d8426dd7f6c783af"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#ae11715606af5b9d6d8426dd7f6c783af">OpenMS::TwoDOptimization::setMaxIterations</a></div><div class="ttdeci">void setMaxIterations(UInt max_iteration)</div><div class="ttdoc">Mutable access to the maximal number of iterations. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:143</div></div>
<div class="ttc" id="structOpenMS_1_1IsotopeCluster_html"><div class="ttname"><a href="structOpenMS_1_1IsotopeCluster.html">OpenMS::IsotopeCluster</a></div><div class="ttdoc">Stores information about an isotopic cluster (i.e. potential peptide charge variants) ...</div><div class="ttdef"><b>Definition:</b> IsotopeCluster.h:45</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors_html"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html">OpenMS::OptimizationFunctions::PenaltyFactors</a></div><div class="ttdoc">Class for the penalty factors used during the optimization. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:71</div></div>
<div class="ttc" id="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet_html_a8253a7962ca1c79b71e6af96589b7720"><div class="ttname"><a href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html#a8253a7962ca1c79b71e6af96589b7720">OpenMS::IsotopeCluster::ChargedIndexSet::charge</a></div><div class="ttdeci">Int charge</div><div class="ttdoc">charge estimate (convention: zero means &quot;no charge estimate&quot;) </div><div class="ttdef"><b>Definition:</b> IsotopeCluster.h:62</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a78c0d505b8706df48e8cf696e21035ee"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a78c0d505b8706df48e8cf696e21035ee">OpenMS::TwoDOptimization::max_iteration_</a></div><div class="ttdeci">UInt max_iteration_</div><div class="ttdoc">Convergence Parameter: Maximal number of iterations. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:222</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html">OpenMS::DefaultParamHandler</a></div><div class="ttdoc">A base class for all classes handling default parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:90</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizePick_1_1Data_html_afc5753d32dfc3c8659038a3e1ac68c86"><div class="ttname"><a href="structOpenMS_1_1OptimizePick_1_1Data.html#afc5753d32dfc3c8659038a3e1ac68c86">OpenMS::OptimizePick::Data::signal</a></div><div class="ttdeci">std::vector< double > signal</div><div class="ttdef"><b>Definition:</b> OptimizePick.h:124</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a4c366f74747bc1983e91ca37d58af808"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a4c366f74747bc1983e91ca37d58af808">OpenMS::TwoDOptimization::getMaxIterations</a></div><div class="ttdeci">UInt getMaxIterations() const </div><div class="ttdoc">Non-mutable access to the maximal number of iterations. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:141</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a8e66c4bb9601b0c87307512a044930b8"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a8e66c4bb9601b0c87307512a044930b8">OpenMS::TwoDOptimization::getMaxAbsError</a></div><div class="ttdeci">DoubleReal getMaxAbsError() const </div><div class="ttdoc">Non-mutable access to the maximal absolute error. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:123</div></div>
<div class="ttc" id="structOpenMS_1_1TwoDOptimization_1_1Data_html_a1e60993834d6cab4067738dfd729dad0"><div class="ttname"><a href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a1e60993834d6cab4067738dfd729dad0">OpenMS::TwoDOptimization::Data::matching_peaks</a></div><div class="ttdeci">std::map< Int, std::vector< PeakIndex > > matching_peaks</div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:190</div></div>
<div class="ttc" id="structOpenMS_1_1PairComparatorFirstElement_html"><div class="ttname"><a href="structOpenMS_1_1PairComparatorFirstElement.html">OpenMS::PairComparatorFirstElement</a></div><div class="ttdoc">Class for comparison of std::pair using first ONLY e.g. for use with std::sort. </div><div class="ttdef"><b>Definition:</b> ComparatorUtils.h:326</div></div>
<div class="ttc" id="classOpenMS_1_1MSSpectrum_html_a57213d8c30f9d5d0d6fb3fb472d21f05"><div class="ttname"><a href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">OpenMS::MSSpectrum::getFloatDataArrays</a></div><div class="ttdeci">const FloatDataArrays & getFloatDataArrays() const </div><div class="ttdoc">Returns a const reference to the float meta data arrays. </div><div class="ttdef"><b>Definition:</b> MSSpectrum.h:270</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_adca2617ab638fed2467b9d57b1fe2cfa"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#adca2617ab638fed2467b9d57b1fe2cfa">OpenMS::TwoDOptimization::optimizeRegionsScanwise_</a></div><div class="ttdeci">void optimizeRegionsScanwise_(InputSpectrumIterator &first, InputSpectrumIterator &last, MSExperiment< OutputPeakType > &ms_exp)</div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:808</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity_html_a5343d7f469d61e6d3f4808a609094175"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html#a5343d7f469d61e6d3f4808a609094175">OpenMS::OptimizationFunctions::PenaltyFactorsIntensity::height</a></div><div class="ttdeci">DoubleReal height</div><div class="ttdef"><b>Definition:</b> OptimizePeakDeconvolution.h:85</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="Exception_8h_html"><div class="ttname"><a href="Exception_8h.html">Exception.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_a5678eb60386afb7f97145b361bd3947f"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#a5678eb60386afb7f97145b361bd3947f">OpenMS::TwoDOptimization::optimize</a></div><div class="ttdeci">void optimize(InputSpectrumIterator first, InputSpectrumIterator last, MSExperiment< OutputPeakType > &ms_exp, bool real2D=true)</div><div class="ttdoc">Find two dimensional peak clusters and optimize their peak parameters. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:286</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html_af4c776b75fd26c91f570e5bb9ef0b4c4"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html#af4c776b75fd26c91f570e5bb9ef0b4c4">OpenMS::TwoDOptimization::evaluate2D_</a></div><div class="ttdeci">static Int evaluate2D_(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J)</div><div class="ttdoc">Function that calls residual2D and jacobian2D*/. </div></div>
<div class="ttc" id="classOpenMS_1_1OptimizePick_html"><div class="ttname"><a href="classOpenMS_1_1OptimizePick.html">OpenMS::OptimizePick</a></div><div class="ttdoc">This class provides the non-linear optimization of the peak parameters. </div><div class="ttdef"><b>Definition:</b> OptimizePick.h:116</div></div>
<div class="ttc" id="classOpenMS_1_1TwoDOptimization_html"><div class="ttname"><a href="classOpenMS_1_1TwoDOptimization.html">OpenMS::TwoDOptimization</a></div><div class="ttdoc">This class provides the two-dimensional optimization of the picked peak parameters. </div><div class="ttdef"><b>Definition:</b> TwoDOptimization.h:86</div></div>
<div class="ttc" id="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity_html"><div class="ttname"><a href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OpenMS::OptimizationFunctions::PenaltyFactorsIntensity</a></div><div class="ttdoc">Class for the penalty factors used during the optimization. </div><div class="ttdef"><b>Definition:</b> OptimizePeakDeconvolution.h:66</div></div>
<div class="ttc" id="group__Concept_html_gace75bfb1aba684e874dffee13738bd15"><div class="ttname"><a href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">OpenMS::DoubleReal</a></div><div class="ttdeci">double DoubleReal</div><div class="ttdoc">Double-precision real type. </div><div class="ttdef"><b>Definition:</b> Types.h:118</div></div>
<div class="ttc" id="structOpenMS_1_1PeakShape_html_a0b633e3762805bc447c451f262a8f405"><div class="ttname"><a href="structOpenMS_1_1PeakShape.html#a0b633e3762805bc447c451f262a8f405">OpenMS::PeakShape::mz_position</a></div><div class="ttdeci">DoubleReal mz_position</div><div class="ttdoc">Centroid position. </div><div class="ttdef"><b>Definition:</b> PeakShape.h:133</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 11:19:22 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>
|
