1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
|
<HTML>
<HEAD>
<TITLE>TwoDOptimization Class Reference</TITLE>
<LINK HREF="doxygen.css" REL="stylesheet" TYPE="text/css">
<LINK HREF="style_ini.css" REL="stylesheet" TYPE="text/css">
</HEAD>
<BODY BGCOLOR="#FFFFFF">
<A href="index.html">Home</A> ·
<A href="classes.html">Classes</A> ·
<A href="annotated.html">Annotated Classes</A> ·
<A href="modules.html">Modules</A> ·
<A href="functions_func.html">Members</A> ·
<A href="namespaces.html">Namespaces</A> ·
<A href="pages.html">Related Pages</A>
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<!-- Generated by Doxygen 1.8.5 -->
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#nested-classes">Classes</a> |
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pro-methods">Protected Member Functions</a> |
<a href="#pro-attribs">Protected Attributes</a> |
<a href="classOpenMS_1_1TwoDOptimization-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">TwoDOptimization Class Reference</div> </div>
</div><!--header-->
<div class="contents">
<p>This class provides the two-dimensional optimization of the picked peak parameters.
<a href="classOpenMS_1_1TwoDOptimization.html#details">More...</a></p>
<p><code>#include <<a class="el" href="TwoDOptimization_8h_source.html">OpenMS/TRANSFORMATIONS/RAW2PEAK/TwoDOptimization.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for TwoDOptimization:</div>
<div class="dyncontent">
<div class="center">
<img src="classOpenMS_1_1TwoDOptimization.png" usemap="#TwoDOptimization_map" alt=""/>
<map id="TwoDOptimization_map" name="TwoDOptimization_map">
<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,133,24"/>
</map>
</div></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html">Data</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">Helper struct (contains the size of an area and a raw data container) <a href="structOpenMS_1_1TwoDOptimization_1_1Data.html#details">More...</a><br/></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a5294b42aa00069784e09174ac698238a"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a5294b42aa00069784e09174ac698238a">TwoDOptimization</a> ()</td></tr>
<tr class="memdesc:a5294b42aa00069784e09174ac698238a"><td class="mdescLeft"> </td><td class="mdescRight">Constructor. <a href="#a5294b42aa00069784e09174ac698238a">More...</a><br/></td></tr>
<tr class="separator:a5294b42aa00069784e09174ac698238a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab3721ba52a2edabdb36248772331cf80"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#ab3721ba52a2edabdb36248772331cf80">TwoDOptimization</a> (const <a class="el" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a> &opt)</td></tr>
<tr class="memdesc:ab3721ba52a2edabdb36248772331cf80"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#ab3721ba52a2edabdb36248772331cf80">More...</a><br/></td></tr>
<tr class="separator:ab3721ba52a2edabdb36248772331cf80"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae71d03ba24d6ab714f95b65a524b9ec4"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#ae71d03ba24d6ab714f95b65a524b9ec4">~TwoDOptimization</a> ()</td></tr>
<tr class="memdesc:ae71d03ba24d6ab714f95b65a524b9ec4"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#ae71d03ba24d6ab714f95b65a524b9ec4">More...</a><br/></td></tr>
<tr class="separator:ae71d03ba24d6ab714f95b65a524b9ec4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab63fbd5d7312e68a05e0c4b0ef5360b5"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#ab63fbd5d7312e68a05e0c4b0ef5360b5">operator=</a> (const <a class="el" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a> &opt)</td></tr>
<tr class="memdesc:ab63fbd5d7312e68a05e0c4b0ef5360b5"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#ab63fbd5d7312e68a05e0c4b0ef5360b5">More...</a><br/></td></tr>
<tr class="separator:ab63fbd5d7312e68a05e0c4b0ef5360b5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aafe5d0ee09d7e6ee8a5f12b9f5f40a19"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#aafe5d0ee09d7e6ee8a5f12b9f5f40a19">getMZTolerance</a> () const </td></tr>
<tr class="memdesc:aafe5d0ee09d7e6ee8a5f12b9f5f40a19"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the matching epsilon. <a href="#aafe5d0ee09d7e6ee8a5f12b9f5f40a19">More...</a><br/></td></tr>
<tr class="separator:aafe5d0ee09d7e6ee8a5f12b9f5f40a19"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aef02420ae0f171972e40c069ec5931be"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#aef02420ae0f171972e40c069ec5931be">setMZTolerance</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> tolerance_mz)</td></tr>
<tr class="memdesc:aef02420ae0f171972e40c069ec5931be"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the matching epsilon. <a href="#aef02420ae0f171972e40c069ec5931be">More...</a><br/></td></tr>
<tr class="separator:aef02420ae0f171972e40c069ec5931be"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:add19caffdc34d20e18e084922846ec3a"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#add19caffdc34d20e18e084922846ec3a">getMaxPeakDistance</a> () const </td></tr>
<tr class="memdesc:add19caffdc34d20e18e084922846ec3a"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the maximal peak distance in a cluster. <a href="#add19caffdc34d20e18e084922846ec3a">More...</a><br/></td></tr>
<tr class="separator:add19caffdc34d20e18e084922846ec3a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afe966e2a453a2c21000f38f431bc6205"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#afe966e2a453a2c21000f38f431bc6205">setMaxPeakDistance</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> max_peak_distance)</td></tr>
<tr class="memdesc:afe966e2a453a2c21000f38f431bc6205"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the maximal peak distance in a cluster. <a href="#afe966e2a453a2c21000f38f431bc6205">More...</a><br/></td></tr>
<tr class="separator:afe966e2a453a2c21000f38f431bc6205"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8e66c4bb9601b0c87307512a044930b8"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a8e66c4bb9601b0c87307512a044930b8">getMaxAbsError</a> () const </td></tr>
<tr class="memdesc:a8e66c4bb9601b0c87307512a044930b8"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the maximal absolute error. <a href="#a8e66c4bb9601b0c87307512a044930b8">More...</a><br/></td></tr>
<tr class="separator:a8e66c4bb9601b0c87307512a044930b8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a850156405bdec2d3a4761d49310151e7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a850156405bdec2d3a4761d49310151e7">setMaxAbsError</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> eps_abs)</td></tr>
<tr class="memdesc:a850156405bdec2d3a4761d49310151e7"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the maximal absolute error. <a href="#a850156405bdec2d3a4761d49310151e7">More...</a><br/></td></tr>
<tr class="separator:a850156405bdec2d3a4761d49310151e7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac061845432fbff0f67d3212a815ebac9"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#ac061845432fbff0f67d3212a815ebac9">getMaxRelError</a> () const </td></tr>
<tr class="memdesc:ac061845432fbff0f67d3212a815ebac9"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the maximal relative error. <a href="#ac061845432fbff0f67d3212a815ebac9">More...</a><br/></td></tr>
<tr class="separator:ac061845432fbff0f67d3212a815ebac9"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6ed5164a8b4af4b3de8e04912350acfb"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a6ed5164a8b4af4b3de8e04912350acfb">setMaxRelError</a> (<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> eps_rel)</td></tr>
<tr class="memdesc:a6ed5164a8b4af4b3de8e04912350acfb"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the maximal relative error. <a href="#a6ed5164a8b4af4b3de8e04912350acfb">More...</a><br/></td></tr>
<tr class="separator:a6ed5164a8b4af4b3de8e04912350acfb"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4c366f74747bc1983e91ca37d58af808"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a4c366f74747bc1983e91ca37d58af808">getMaxIterations</a> () const </td></tr>
<tr class="memdesc:a4c366f74747bc1983e91ca37d58af808"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the maximal number of iterations. <a href="#a4c366f74747bc1983e91ca37d58af808">More...</a><br/></td></tr>
<tr class="separator:a4c366f74747bc1983e91ca37d58af808"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae11715606af5b9d6d8426dd7f6c783af"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#ae11715606af5b9d6d8426dd7f6c783af">setMaxIterations</a> (<a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> max_iteration)</td></tr>
<tr class="memdesc:ae11715606af5b9d6d8426dd7f6c783af"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the maximal number of iterations. <a href="#ae11715606af5b9d6d8426dd7f6c783af">More...</a><br/></td></tr>
<tr class="separator:ae11715606af5b9d6d8426dd7f6c783af"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aacb90f036a8fff25704290ac0c34364c"><td class="memItemLeft" align="right" valign="top">const <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#aacb90f036a8fff25704290ac0c34364c">getPenalties</a> () const </td></tr>
<tr class="memdesc:aacb90f036a8fff25704290ac0c34364c"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the minimal number of adjacent scans. <a href="#aacb90f036a8fff25704290ac0c34364c">More...</a><br/></td></tr>
<tr class="separator:aacb90f036a8fff25704290ac0c34364c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a165bfd792d0e5b693e0cdd6a9782d27f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a165bfd792d0e5b693e0cdd6a9782d27f">setPenalties</a> (<a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a> &penalties)</td></tr>
<tr class="memdesc:a165bfd792d0e5b693e0cdd6a9782d27f"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the minimal number of adjacent scans. <a href="#a165bfd792d0e5b693e0cdd6a9782d27f">More...</a><br/></td></tr>
<tr class="separator:a165bfd792d0e5b693e0cdd6a9782d27f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5678eb60386afb7f97145b361bd3947f"><td class="memTemplParams" colspan="2">template<typename InputSpectrumIterator , typename OutputPeakType > </td></tr>
<tr class="memitem:a5678eb60386afb7f97145b361bd3947f"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a5678eb60386afb7f97145b361bd3947f">optimize</a> (InputSpectrumIterator first, InputSpectrumIterator last, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< OutputPeakType > &ms_exp, bool real2D=true)</td></tr>
<tr class="memdesc:a5678eb60386afb7f97145b361bd3947f"><td class="mdescLeft"> </td><td class="mdescRight">Find two dimensional peak clusters and optimize their peak parameters. <a href="#a5678eb60386afb7f97145b361bd3947f">More...</a><br/></td></tr>
<tr class="separator:a5678eb60386afb7f97145b361bd3947f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pub_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Constructor with name that is displayed in error messages. <a href="#afb6802fda161cb0c1a4a05597f94aecc">More...</a><br/></td></tr>
<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a954da7eef3cfddda446574eaadd20abb">More...</a><br/></td></tr>
<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a> ()</td></tr>
<tr class="memdesc:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a11e9d6dd34fe8860874aa8abe0ec121b">More...</a><br/></td></tr>
<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">operator=</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
<tr class="memdesc:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#ae6b6d68036a573a44f6609460ba2dfb6">More...</a><br/></td></tr>
<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs) const </td></tr>
<tr class="memdesc:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#ac435f2dd4d9f9328db83af97129a8d7e">More...</a><br/></td></tr>
<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &param)</td></tr>
<tr class="memdesc:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Sets the parameters. <a href="#abc8067511cfc949ae942ea2b08588f81">More...</a><br/></td></tr>
<tr class="separator:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a> () const </td></tr>
<tr class="memdesc:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the parameters. <a href="#a7f6aab5a7dfbdd1c062a4352a29361f3">More...</a><br/></td></tr>
<tr class="separator:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a> () const </td></tr>
<tr class="memdesc:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the default parameters. <a href="#a02f02fa9832ca3e8d47c575a39803a2a">More...</a><br/></td></tr>
<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a> () const </td></tr>
<tr class="memdesc:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the name. <a href="#aaee0f2845288173de9f6ad47e6ad31d5">More...</a><br/></td></tr>
<tr class="separator:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
<tr class="memdesc:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the name. <a href="#a77d37f2e1c12e8bd33ea0e660a89e927">More...</a><br/></td></tr>
<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a> () const </td></tr>
<tr class="memdesc:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the registered subsections. <a href="#a768d4a2093627a2f34728656a9721bdf">More...</a><br/></td></tr>
<tr class="separator:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr class="memitem:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#aaf258e1a9846d9b238ee4b3005ad3ee9">updateMembers_</a> ()</td></tr>
<tr class="memdesc:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="mdescLeft"> </td><td class="mdescRight">update members method from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. ">DefaultParamHandler</a> to update the members <a href="#aaf258e1a9846d9b238ee4b3005ad3ee9">More...</a><br/></td></tr>
<tr class="separator:aaf258e1a9846d9b238ee4b3005ad3ee9"><td class="memSeparator" colspan="2"> </td></tr>
<tr><td colspan="2"><div class="groupHeader">Auxiliary Functions for the search of matching regions</div></td></tr>
<tr class="memitem:a74f373ec1e1e803064c86d9b0f18abdd"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> >::iterator </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a74f373ec1e1e803064c86d9b0f18abdd">searchInScan_</a> (std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> >::iterator scan_begin, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> >::iterator scan_end, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> current_mz)</td></tr>
<tr class="separator:a74f373ec1e1e803064c86d9b0f18abdd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a17e2d6f48048565ca00dee8f87da38ba"><td class="memTemplParams" colspan="2">template<typename InputSpectrumIterator , typename OutputPeakType > </td></tr>
<tr class="memitem:a17e2d6f48048565ca00dee8f87da38ba"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">optimizeRegions_</a> (InputSpectrumIterator &first, InputSpectrumIterator &last, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< OutputPeakType > &ms_exp)</td></tr>
<tr class="separator:a17e2d6f48048565ca00dee8f87da38ba"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adca2617ab638fed2467b9d57b1fe2cfa"><td class="memTemplParams" colspan="2">template<typename InputSpectrumIterator , typename OutputPeakType > </td></tr>
<tr class="memitem:adca2617ab638fed2467b9d57b1fe2cfa"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#adca2617ab638fed2467b9d57b1fe2cfa">optimizeRegionsScanwise_</a> (InputSpectrumIterator &first, InputSpectrumIterator &last, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< OutputPeakType > &ms_exp)</td></tr>
<tr class="separator:adca2617ab638fed2467b9d57b1fe2cfa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6d2b21b20b10f65e5a6052e8c8aa84e7"><td class="memTemplParams" colspan="2">template<typename InputSpectrumIterator , typename OutputPeakType > </td></tr>
<tr class="memitem:a6d2b21b20b10f65e5a6052e8c8aa84e7"><td class="memTemplItemLeft" align="right" valign="top">void </td><td class="memTemplItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a6d2b21b20b10f65e5a6052e8c8aa84e7">getRegionEndpoints_</a> (<a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< OutputPeakType > &exp, InputSpectrumIterator &first, InputSpectrumIterator &last, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> iso_map_idx, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> noise_level, <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html">TwoDOptimization::Data</a> &d)</td></tr>
<tr class="memdesc:a6d2b21b20b10f65e5a6052e8c8aa84e7"><td class="mdescLeft"> </td><td class="mdescRight">Get the indices of the first and last raw data point of this region. <a href="#a6d2b21b20b10f65e5a6052e8c8aa84e7">More...</a><br/></td></tr>
<tr class="separator:a6d2b21b20b10f65e5a6052e8c8aa84e7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8e4d88640e61ef82005212a8583ba784"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a8e4d88640e61ef82005212a8583ba784">findMatchingPeaks_</a> (std::multimap< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="structOpenMS_1_1IsotopeCluster.html">IsotopeCluster</a> >::iterator &it, <a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><> &ms_exp)</td></tr>
<tr class="memdesc:a8e4d88640e61ef82005212a8583ba784"><td class="mdescLeft"> </td><td class="mdescRight">Identify matching peak in a peak cluster. <a href="#a8e4d88640e61ef82005212a8583ba784">More...</a><br/></td></tr>
<tr class="separator:a8e4d88640e61ef82005212a8583ba784"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a> ()</td></tr>
<tr class="memdesc:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Updates the parameters after the defaults have been set in the constructor. <a href="#a2802c591e6d7fd3fd9cc35f5e875d0ba">More...</a><br/></td></tr>
<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-static-methods"></a>
Static Protected Member Functions</h2></td></tr>
<tr><td colspan="2"><div class="groupHeader">Functions provided to the gsl Levenberg-Marquardt</div></td></tr>
<tr class="memitem:aa82b642dc0b200f292a5f44e6458bf16"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#aa82b642dc0b200f292a5f44e6458bf16">residual2D_</a> (const gsl_vector *x, void *params, gsl_vector *f)</td></tr>
<tr class="memdesc:aa82b642dc0b200f292a5f44e6458bf16"><td class="mdescLeft"> </td><td class="mdescRight">Function computing estimated signal and its deviation to the experimental signal*/. <a href="#aa82b642dc0b200f292a5f44e6458bf16">More...</a><br/></td></tr>
<tr class="separator:aa82b642dc0b200f292a5f44e6458bf16"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab25862b6e7eaee9e6739c52ae57d0896"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#ab25862b6e7eaee9e6739c52ae57d0896">jacobian2D_</a> (const gsl_vector *x, void *params, gsl_matrix *J)</td></tr>
<tr class="memdesc:ab25862b6e7eaee9e6739c52ae57d0896"><td class="mdescLeft"> </td><td class="mdescRight">Function computing the Jacobian */. <a href="#ab25862b6e7eaee9e6739c52ae57d0896">More...</a><br/></td></tr>
<tr class="separator:ab25862b6e7eaee9e6739c52ae57d0896"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af4c776b75fd26c91f570e5bb9ef0b4c4"><td class="memItemLeft" align="right" valign="top">static <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#af4c776b75fd26c91f570e5bb9ef0b4c4">evaluate2D_</a> (const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J)</td></tr>
<tr class="memdesc:af4c776b75fd26c91f570e5bb9ef0b4c4"><td class="mdescLeft"> </td><td class="mdescRight">Function that calls residual2D and jacobian2D*/. <a href="#af4c776b75fd26c91f570e5bb9ef0b4c4">More...</a><br/></td></tr>
<tr class="separator:af4c776b75fd26c91f570e5bb9ef0b4c4"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr class="memitem:a0c0b2f69c6c06fae06bd27ff373b07f0"><td class="memItemLeft" align="right" valign="top">std::multimap< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1IsotopeCluster.html">IsotopeCluster</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">iso_map_</a></td></tr>
<tr class="memdesc:a0c0b2f69c6c06fae06bd27ff373b07f0"><td class="mdescLeft"> </td><td class="mdescRight">stores the retention time of each isotopic cluster <a href="#a0c0b2f69c6c06fae06bd27ff373b07f0">More...</a><br/></td></tr>
<tr class="separator:a0c0b2f69c6c06fae06bd27ff373b07f0"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af0c0642cd0366fd192034cf58036fb11"><td class="memItemLeft" align="right" valign="top">std::multimap< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <br class="typebreak"/>
<a class="el" href="structOpenMS_1_1IsotopeCluster.html">IsotopeCluster</a> ><br class="typebreak"/>
::const_iterator </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#af0c0642cd0366fd192034cf58036fb11">curr_region_</a></td></tr>
<tr class="memdesc:af0c0642cd0366fd192034cf58036fb11"><td class="mdescLeft"> </td><td class="mdescRight">Pointer to the current region. <a href="#af0c0642cd0366fd192034cf58036fb11">More...</a><br/></td></tr>
<tr class="separator:af0c0642cd0366fd192034cf58036fb11"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a58b5225db8586aea7dd011a7447de6af"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a58b5225db8586aea7dd011a7447de6af">max_peak_distance_</a></td></tr>
<tr class="memdesc:a58b5225db8586aea7dd011a7447de6af"><td class="mdescLeft"> </td><td class="mdescRight">upper bound for distance between two peaks belonging to the same region <a href="#a58b5225db8586aea7dd011a7447de6af">More...</a><br/></td></tr>
<tr class="separator:a58b5225db8586aea7dd011a7447de6af"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acbc4c0b42c88614c321ed3a8e4075c08"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#acbc4c0b42c88614c321ed3a8e4075c08">tolerance_mz_</a></td></tr>
<tr class="memdesc:acbc4c0b42c88614c321ed3a8e4075c08"><td class="mdescLeft"> </td><td class="mdescRight">threshold for the difference in the peak position of two matching peaks <a href="#acbc4c0b42c88614c321ed3a8e4075c08">More...</a><br/></td></tr>
<tr class="separator:acbc4c0b42c88614c321ed3a8e4075c08"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a50d07207174c609658e117b2aa89cb10"><td class="memItemLeft" align="right" valign="top">std::map< <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, std::vector<br class="typebreak"/>
< <a class="el" href="structOpenMS_1_1PeakIndex.html">PeakIndex</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a50d07207174c609658e117b2aa89cb10">matching_peaks_</a></td></tr>
<tr class="memdesc:a50d07207174c609658e117b2aa89cb10"><td class="mdescLeft"> </td><td class="mdescRight">Indices of peaks in the adjacent scans matching peaks in the scan with no. ref_scan. <a href="#a50d07207174c609658e117b2aa89cb10">More...</a><br/></td></tr>
<tr class="separator:a50d07207174c609658e117b2aa89cb10"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1ba9944277216253f5225aa74581147e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a1ba9944277216253f5225aa74581147e">eps_abs_</a></td></tr>
<tr class="memdesc:a1ba9944277216253f5225aa74581147e"><td class="mdescLeft"> </td><td class="mdescRight">Convergence Parameter: Maximal absolute error. <a href="#a1ba9944277216253f5225aa74581147e">More...</a><br/></td></tr>
<tr class="separator:a1ba9944277216253f5225aa74581147e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0409337ea8ad2ae8fde8f6cba1e889a2"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a0409337ea8ad2ae8fde8f6cba1e889a2">eps_rel_</a></td></tr>
<tr class="memdesc:a0409337ea8ad2ae8fde8f6cba1e889a2"><td class="mdescLeft"> </td><td class="mdescRight">Convergence Parameter: Maximal relative error. <a href="#a0409337ea8ad2ae8fde8f6cba1e889a2">More...</a><br/></td></tr>
<tr class="separator:a0409337ea8ad2ae8fde8f6cba1e889a2"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a78c0d505b8706df48e8cf696e21035ee"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a78c0d505b8706df48e8cf696e21035ee">max_iteration_</a></td></tr>
<tr class="memdesc:a78c0d505b8706df48e8cf696e21035ee"><td class="mdescLeft"> </td><td class="mdescRight">Convergence Parameter: Maximal number of iterations. <a href="#a78c0d505b8706df48e8cf696e21035ee">More...</a><br/></td></tr>
<tr class="separator:a78c0d505b8706df48e8cf696e21035ee"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5ecbb7085dd05993affbe76a8eae8718"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a5ecbb7085dd05993affbe76a8eae8718">real_2D_</a></td></tr>
<tr class="memdesc:a5ecbb7085dd05993affbe76a8eae8718"><td class="mdescLeft"> </td><td class="mdescRight">Optimization considering all scans of a cluster or optimization of each scan separately. <a href="#a5ecbb7085dd05993affbe76a8eae8718">More...</a><br/></td></tr>
<tr class="separator:a5ecbb7085dd05993affbe76a8eae8718"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1491750eda19a5fae8d6aa0deafb60ce"><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1TwoDOptimization.html#a1491750eda19a5fae8d6aa0deafb60ce">penalties_</a></td></tr>
<tr class="memdesc:a1491750eda19a5fae8d6aa0deafb60ce"><td class="mdescLeft"> </td><td class="mdescRight">Penalty factors for some parameters in the optimization. <a href="#a1491750eda19a5fae8d6aa0deafb60ce">More...</a><br/></td></tr>
<tr class="separator:a1491750eda19a5fae8d6aa0deafb60ce"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="inherit_header pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
<tr class="separator:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td></tr>
<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
<tr class="separator:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
<tr class="separator:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td></tr>
<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
<tr class="separator:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
<tr class="separator:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
<tr class="separator:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>This class provides the two-dimensional optimization of the picked peak parameters. </p>
<p>Given the picked peaks, this class optimizes the peak parameters of each isotope pattern using a non-linear optimization. The peaks of adjacent scans are adjusted to achieve that a peak occuring in several scans has always the same m/z position. For the optimization the Levenberg-Marquardt algorithm provided from the GSL is used. The optimized parameters are the m/z values, the left and right width, which shall be equal for a peak in all scans, and the peaks' heights.</p>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000026">Todo:</a></b></dt><dd>Works only with defined types due to pointers to the data in the optimization namespace! Change that or remove templates (Alexandra)</dd></dl>
<B>Parameters of this class are:</B><BR><BR>
<table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
<tr style="border-bottom:1px solid black; background:#fffff0"><th>Name</th><th>Type</th><th>Default</th><th>Restrictions</th><th>Description</th></tr>
<tr>
<td style="vertical-align:top"><i>delta_abs_error</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">9.99999974737875e-06</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">if the absolute error gets smaller than this value the fitting is stopped.</td>
</tr>
<tr>
<td style="vertical-align:top"><i>delta_rel_error</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">9.99999974737875e-06</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">if the relative error gets smaller than this value the fitting is stopped.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>iterations</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">10</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">maximal number of iterations for the fitting step</td>
</tr>
<tr>
<td style="vertical-align:top"><b>penalties:position</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">If the position changes more than 0.2Da during the fitting it can be penalized</td>
</tr>
<tr>
<td style="vertical-align:top"><b>penalties:height</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>penalties:left_width</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized.</td>
</tr>
<tr>
<td style="vertical-align:top"><b>penalties:right_width</b></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">0</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized.</td>
</tr>
<tr>
<td style="vertical-align:top"><i>2d:tolerance_mz</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">2.2</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">mz tolerance for cluster construction</td>
</tr>
<tr>
<td style="vertical-align:top"><i>2d:max_peak_distance</i></td>
<td style="vertical-align:top">float</td><td style="vertical-align:top">1.2</td>
<td style="vertical-align:top"> </td><td style="vertical-align:top">maximal peak distance in mz in a cluster</td>
</tr>
</table>
<br>
<b>Note:</b>
<UL style="margin-top:0px;">
<LI> If a section name is documented, the documentation is displayed as tooltip.
<LI> Advanced parameter names are italic.
</UL>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a class="anchor" id="a5294b42aa00069784e09174ac698238a"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Constructor. </p>
</div>
</div>
<a class="anchor" id="ab3721ba52a2edabdb36248772331cf80"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a> & </td>
<td class="paramname"><em>opt</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Copy constructor. </p>
</div>
</div>
<a class="anchor" id="ae71d03ba24d6ab714f95b65a524b9ec4"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">virtual ~<a class="el" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span><span class="mlabel">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Destructor. </p>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a class="anchor" id="af4c776b75fd26c91f570e5bb9ef0b4c4"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">static <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> evaluate2D_ </td>
<td>(</td>
<td class="paramtype">const gsl_vector * </td>
<td class="paramname"><em>x</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">void * </td>
<td class="paramname"><em>params</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">gsl_vector * </td>
<td class="paramname"><em>f</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">gsl_matrix * </td>
<td class="paramname"><em>J</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">static</span><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Function that calls residual2D and jacobian2D*/. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_()</a>.</p>
</div>
</div>
<a class="anchor" id="a8e4d88640e61ef82005212a8583ba784"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void findMatchingPeaks_ </td>
<td>(</td>
<td class="paramtype">std::multimap< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="structOpenMS_1_1IsotopeCluster.html">IsotopeCluster</a> >::iterator & </td>
<td class="paramname"><em>it</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a><> & </td>
<td class="paramname"><em>ms_exp</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Identify matching peak in a peak cluster. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_()</a>.</p>
</div>
</div>
<a class="anchor" id="a8e66c4bb9601b0c87307512a044930b8"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getMaxAbsError </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Non-mutable access to the maximal absolute error. </p>
</div>
</div>
<a class="anchor" id="a4c366f74747bc1983e91ca37d58af808"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> getMaxIterations </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Non-mutable access to the maximal number of iterations. </p>
</div>
</div>
<a class="anchor" id="add19caffdc34d20e18e084922846ec3a"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getMaxPeakDistance </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Non-mutable access to the maximal peak distance in a cluster. </p>
</div>
</div>
<a class="anchor" id="ac061845432fbff0f67d3212a815ebac9"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getMaxRelError </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Non-mutable access to the maximal relative error. </p>
</div>
</div>
<a class="anchor" id="aafe5d0ee09d7e6ee8a5f12b9f5f40a19"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> getMZTolerance </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Non-mutable access to the matching epsilon. </p>
</div>
</div>
<a class="anchor" id="aacb90f036a8fff25704290ac0c34364c"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">const <a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a>& getPenalties </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Non-mutable access to the minimal number of adjacent scans. </p>
</div>
</div>
<a class="anchor" id="a6d2b21b20b10f65e5a6052e8c8aa84e7"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void getRegionEndpoints_ </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< OutputPeakType > & </td>
<td class="paramname"><em>exp</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">InputSpectrumIterator & </td>
<td class="paramname"><em>first</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">InputSpectrumIterator & </td>
<td class="paramname"><em>last</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td>
<td class="paramname"><em>iso_map_idx</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>noise_level</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html">TwoDOptimization::Data</a> & </td>
<td class="paramname"><em>d</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Get the indices of the first and last raw data point of this region. </p>
<p>References <a class="el" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">MSExperiment< PeakT, ChromatogramPeakT >::begin()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">MSExperiment< PeakT, ChromatogramPeakT >::end()</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">TwoDOptimization::iso_map_</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#adb2f0f3e10754ca4dc7be677f15689a3">MSExperiment< PeakT, ChromatogramPeakT >::RTBegin()</a>, <a class="el" href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">MSSpectrum< PeakT >::setRT()</a>, <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">TwoDOptimization::Data::signal2D</a>, and <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_()</a>, and <a class="el" href="classOpenMS_1_1TwoDOptimization.html#adca2617ab638fed2467b9d57b1fe2cfa">TwoDOptimization::optimizeRegionsScanwise_()</a>.</p>
</div>
</div>
<a class="anchor" id="ab25862b6e7eaee9e6739c52ae57d0896"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">static <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> jacobian2D_ </td>
<td>(</td>
<td class="paramtype">const gsl_vector * </td>
<td class="paramname"><em>x</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">void * </td>
<td class="paramname"><em>params</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">gsl_matrix * </td>
<td class="paramname"><em>J</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">static</span><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Function computing the Jacobian */. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_()</a>.</p>
</div>
</div>
<a class="anchor" id="ab63fbd5d7312e68a05e0c4b0ef5360b5"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a>& operator= </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1TwoDOptimization.html">TwoDOptimization</a> & </td>
<td class="paramname"><em>opt</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Assignment operator. </p>
</div>
</div>
<a class="anchor" id="a5678eb60386afb7f97145b361bd3947f"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void optimize </td>
<td>(</td>
<td class="paramtype">InputSpectrumIterator </td>
<td class="paramname"><em>first</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">InputSpectrumIterator </td>
<td class="paramname"><em>last</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< OutputPeakType > & </td>
<td class="paramname"><em>ms_exp</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"><em>real2D</em> = <code>true</code> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Find two dimensional peak clusters and optimize their peak parameters. </p>
<dl class="section note"><dt>Note</dt><dd>For the peak spectra, the following meta data arrays (see <a class="el" href="classOpenMS_1_1MSSpectrum.html" title="The representation of a 1D spectrum. ">MSSpectrum</a>) have to be present and have to be named just as listed here:<ul>
<li>intensity (index:1)</li>
<li>leftWidth (index:3)</li>
<li>rightWidth (index:4)</li>
<li>peakShape (index:5)</li>
</ul>
</dd></dl>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">first</td><td>begin of the raw data spectra iterator range </td></tr>
<tr><td class="paramname">last</td><td>end of the raw data spectra interator range </td></tr>
<tr><td class="paramname">ms_exp</td><td>peak map corresponding to the raw data in the range from <code>first</code> to <code>last</code> </td></tr>
<tr><td class="paramname">real2D</td><td>flag if the optimization should be two dimensional or on each scan separately </td></tr>
</table>
</dd>
</dl>
<dl class="exception"><dt>Exceptions</dt><dd>
<table class="exception">
<tr><td class="paramname"><a class="el" href="classOpenMS_1_1Exception_1_1IllegalArgument.html" title="A method or algorithm argument contains illegal values. ">Exception::IllegalArgument</a></td><td>is thrown if required meta information from peak picking is missing (area, shape, left width, right width) or if the input data is invalid in some other way </td></tr>
</table>
</dd>
</dl>
<p>References <a class="el" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">MSExperiment< PeakT, ChromatogramPeakT >::begin()</a>, <a class="el" href="structOpenMS_1_1IsotopeCluster_1_1ChargedIndexSet.html#a8253a7962ca1c79b71e6af96589b7720">IsotopeCluster::ChargedIndexSet::charge</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#af0c0642cd0366fd192034cf58036fb11">TwoDOptimization::curr_region_</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ac6e61de369e994009e36f344f99c15ad">MSExperiment< PeakT, ChromatogramPeakT >::empty()</a>, <a class="el" href="classOpenMS_1_1MSExperiment.html#ab45dae688fc5d8983727abffa4389003">MSExperiment< PeakT, ChromatogramPeakT >::end()</a>, <a class="el" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">Param::getValue()</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">TwoDOptimization::iso_map_</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a58b5225db8586aea7dd011a7447de6af">TwoDOptimization::max_peak_distance_</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_()</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#adca2617ab638fed2467b9d57b1fe2cfa">TwoDOptimization::optimizeRegionsScanwise_()</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">DefaultParamHandler::param_</a>, <a class="el" href="structOpenMS_1_1IsotopeCluster.html#ad4c8689a4cd1334e0eccdadcb0cc5a54">IsotopeCluster::peaks</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a5ecbb7085dd05993affbe76a8eae8718">TwoDOptimization::real_2D_</a>, <a class="el" href="structOpenMS_1_1IsotopeCluster.html#a47b3744693f84a7d94f7181676f36758">IsotopeCluster::scans</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a74f373ec1e1e803064c86d9b0f18abdd">TwoDOptimization::searchInScan_()</a>, <a class="el" href="classOpenMS_1_1MSSpectrum.html#aac8c50f318154e9e5b7b01aee806e17f">MSSpectrum< PeakT >::setRT()</a>, and <a class="el" href="classOpenMS_1_1MSExperiment.html#a9d78a687cf2a391198bb3cbc08bc06cb">MSExperiment< PeakT, ChromatogramPeakT >::size()</a>.</p>
</div>
</div>
<a class="anchor" id="a17e2d6f48048565ca00dee8f87da38ba"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void optimizeRegions_ </td>
<td>(</td>
<td class="paramtype">InputSpectrumIterator & </td>
<td class="paramname"><em>first</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">InputSpectrumIterator & </td>
<td class="paramname"><em>last</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< OutputPeakType > & </td>
<td class="paramname"><em>ms_exp</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Performs 2D optimization of all regions </p>
<p>References <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a1ba9944277216253f5225aa74581147e">TwoDOptimization::eps_abs_</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a0409337ea8ad2ae8fde8f6cba1e889a2">TwoDOptimization::eps_rel_</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#af4c776b75fd26c91f570e5bb9ef0b4c4">TwoDOptimization::evaluate2D_()</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a8e4d88640e61ef82005212a8583ba784">TwoDOptimization::findMatchingPeaks_()</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a6d2b21b20b10f65e5a6052e8c8aa84e7">TwoDOptimization::getRegionEndpoints_()</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">TwoDOptimization::iso_map_</a>, <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">TwoDOptimization::Data::iso_map_iter</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#ab25862b6e7eaee9e6739c52ae57d0896">TwoDOptimization::jacobian2D_()</a>, <a class="el" href="namespaceOpenMS_1_1Constants.html#a93a8dc068053ec44ee7e45864ef969f7">OpenMS::Constants::k</a>, <a class="el" href="structOpenMS_1_1PeakShape.html#a1d1cfd8ffb84e947f82999c682b666a7a6ba0b50b9f0f84a5ad13827c57240f76">PeakShape::LORENTZ_PEAK</a>, <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a1e60993834d6cab4067738dfd729dad0">TwoDOptimization::Data::matching_peaks</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a50d07207174c609658e117b2aa89cb10">TwoDOptimization::matching_peaks_</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a78c0d505b8706df48e8cf696e21035ee">TwoDOptimization::max_iteration_</a>, <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a4dbfc949c1c63f8a02dafd6a592d7955">TwoDOptimization::Data::penalties</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a1491750eda19a5fae8d6aa0deafb60ce">TwoDOptimization::penalties_</a>, <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a2dcab4dd664c2b08f478ebde32edaa74">TwoDOptimization::Data::picked_peaks</a>, <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a16930394d61d06ff8227219211874592">TwoDOptimization::Data::raw_data_first</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#aa82b642dc0b200f292a5f44e6458bf16">TwoDOptimization::residual2D_()</a>, <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">TwoDOptimization::Data::signal2D</a>, and <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a9d5caa74a619fd37c7352fce078259fd">TwoDOptimization::Data::total_nr_peaks</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a5678eb60386afb7f97145b361bd3947f">TwoDOptimization::optimize()</a>.</p>
</div>
</div>
<a class="anchor" id="adca2617ab638fed2467b9d57b1fe2cfa"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void optimizeRegionsScanwise_ </td>
<td>(</td>
<td class="paramtype">InputSpectrumIterator & </td>
<td class="paramname"><em>first</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">InputSpectrumIterator & </td>
<td class="paramname"><em>last</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classOpenMS_1_1MSExperiment.html">MSExperiment</a>< OutputPeakType > & </td>
<td class="paramname"><em>ms_exp</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Performs an optimization of all regions by calling <a class="el" href="classOpenMS_1_1OptimizePick.html" title="This class provides the non-linear optimization of the peak parameters. ">OptimizePick</a> </p>
<p>References <a class="el" href="classOpenMS_1_1MSExperiment.html#a2387033802383edbdc95f9bbb12a707e">MSExperiment< PeakT, ChromatogramPeakT >::begin()</a>, <a class="el" href="classOpenMS_1_1MSSpectrum.html#a57213d8c30f9d5d0d6fb3fb472d21f05">MSSpectrum< PeakT >::getFloatDataArrays()</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a6d2b21b20b10f65e5a6052e8c8aa84e7">TwoDOptimization::getRegionEndpoints_()</a>, <a class="el" href="classOpenMS_1_1Param.html#abd0f5571675ec99e1aa647b39e2a8711">Param::getValue()</a>, <a class="el" href="structOpenMS_1_1PeakShape.html#a5343d7f469d61e6d3f4808a609094175">PeakShape::height</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a0c0b2f69c6c06fae06bd27ff373b07f0">TwoDOptimization::iso_map_</a>, <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#ad777935432d69859f870fd8cc1af7638">TwoDOptimization::Data::iso_map_iter</a>, <a class="el" href="structOpenMS_1_1PeakShape.html#a6bd93679898a199380f450a9351fde28">PeakShape::left_width</a>, <a class="el" href="structOpenMS_1_1PeakShape.html#a1d1cfd8ffb84e947f82999c682b666a7a6ba0b50b9f0f84a5ad13827c57240f76">PeakShape::LORENTZ_PEAK</a>, <a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#abb10592f0ea83f824c0a14f4afa95be4">PenaltyFactors::lWidth</a>, <a class="el" href="structOpenMS_1_1PeakShape.html#a0b633e3762805bc447c451f262a8f405">PeakShape::mz_position</a>, <a class="el" href="classOpenMS_1_1OptimizePick.html#ae69ba4a78f94acc6d88ec067397bf490">OptimizePick::optimize()</a>, <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">DefaultParamHandler::param_</a>, <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a2dcab4dd664c2b08f478ebde32edaa74">TwoDOptimization::Data::picked_peaks</a>, <a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a5e9dd75fc35bca3ebe4981821077aebe">PenaltyFactors::pos</a>, <a class="el" href="structOpenMS_1_1OptimizePick_1_1Data.html#a649cc300c964845ccc272fd2229b6ed4">OptimizePick::Data::positions</a>, <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a16930394d61d06ff8227219211874592">TwoDOptimization::Data::raw_data_first</a>, <a class="el" href="structOpenMS_1_1PeakShape.html#aee68061fb00b7a84b354bac91e492039">PeakShape::right_width</a>, <a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a478a632c0b5a363e215061428eee1a1c">PenaltyFactors::rWidth</a>, <a class="el" href="structOpenMS_1_1OptimizePick_1_1Data.html#afc5753d32dfc3c8659038a3e1ac68c86">OptimizePick::Data::signal</a>, and <a class="el" href="structOpenMS_1_1TwoDOptimization_1_1Data.html#a0aa2a591a3184b849b2dceb401790f2c">TwoDOptimization::Data::signal2D</a>.</p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a5678eb60386afb7f97145b361bd3947f">TwoDOptimization::optimize()</a>.</p>
</div>
</div>
<a class="anchor" id="aa82b642dc0b200f292a5f44e6458bf16"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">static <a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> residual2D_ </td>
<td>(</td>
<td class="paramtype">const gsl_vector * </td>
<td class="paramname"><em>x</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">void * </td>
<td class="paramname"><em>params</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">gsl_vector * </td>
<td class="paramname"><em>f</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">static</span><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Function computing estimated signal and its deviation to the experimental signal*/. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_()</a>.</p>
</div>
</div>
<a class="anchor" id="a74f373ec1e1e803064c86d9b0f18abdd"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::vector<<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>>::iterator searchInScan_ </td>
<td>(</td>
<td class="paramtype">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> >::iterator </td>
<td class="paramname"><em>scan_begin</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> >::iterator </td>
<td class="paramname"><em>scan_end</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>current_mz</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a5678eb60386afb7f97145b361bd3947f">TwoDOptimization::optimize()</a>.</p>
</div>
</div>
<a class="anchor" id="a850156405bdec2d3a4761d49310151e7"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void setMaxAbsError </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>eps_abs</em></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Mutable access to the maximal absolute error. </p>
</div>
</div>
<a class="anchor" id="ae11715606af5b9d6d8426dd7f6c783af"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void setMaxIterations </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> </td>
<td class="paramname"><em>max_iteration</em></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Mutable access to the maximal number of iterations. </p>
</div>
</div>
<a class="anchor" id="afe966e2a453a2c21000f38f431bc6205"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void setMaxPeakDistance </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>max_peak_distance</em></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Mutable access to the maximal peak distance in a cluster. </p>
</div>
</div>
<a class="anchor" id="a6ed5164a8b4af4b3de8e04912350acfb"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void setMaxRelError </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>eps_rel</em></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Mutable access to the maximal relative error. </p>
</div>
</div>
<a class="anchor" id="aef02420ae0f171972e40c069ec5931be"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void setMZTolerance </td>
<td>(</td>
<td class="paramtype"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> </td>
<td class="paramname"><em>tolerance_mz</em></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Mutable access to the matching epsilon. </p>
</div>
</div>
<a class="anchor" id="a165bfd792d0e5b693e0cdd6a9782d27f"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void setPenalties </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a> & </td>
<td class="paramname"><em>penalties</em></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">inline</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Mutable access to the minimal number of adjacent scans. </p>
<p>References <a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html#a5343d7f469d61e6d3f4808a609094175">PenaltyFactorsIntensity::height</a>, <a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#abb10592f0ea83f824c0a14f4afa95be4">PenaltyFactors::lWidth</a>, <a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a5e9dd75fc35bca3ebe4981821077aebe">PenaltyFactors::pos</a>, and <a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactors.html#a478a632c0b5a363e215061428eee1a1c">PenaltyFactors::rWidth</a>.</p>
</div>
</div>
<a class="anchor" id="aaf258e1a9846d9b238ee4b3005ad3ee9"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void updateMembers_ </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span><span class="mlabel">virtual</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>update members method from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. ">DefaultParamHandler</a> to update the members </p>
<p>Reimplemented from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">DefaultParamHandler</a>.</p>
</div>
</div>
<h2 class="groupheader">Member Data Documentation</h2>
<a class="anchor" id="af0c0642cd0366fd192034cf58036fb11"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::multimap<<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="structOpenMS_1_1IsotopeCluster.html">IsotopeCluster</a>>::const_iterator curr_region_</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Pointer to the current region. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a5678eb60386afb7f97145b361bd3947f">TwoDOptimization::optimize()</a>.</p>
</div>
</div>
<a class="anchor" id="a1ba9944277216253f5225aa74581147e"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> eps_abs_</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Convergence Parameter: Maximal absolute error. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_()</a>.</p>
</div>
</div>
<a class="anchor" id="a0409337ea8ad2ae8fde8f6cba1e889a2"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> eps_rel_</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Convergence Parameter: Maximal relative error. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_()</a>.</p>
</div>
</div>
<a class="anchor" id="a0c0b2f69c6c06fae06bd27ff373b07f0"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::multimap<<a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="structOpenMS_1_1IsotopeCluster.html">IsotopeCluster</a>> iso_map_</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>stores the retention time of each isotopic cluster </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a6d2b21b20b10f65e5a6052e8c8aa84e7">TwoDOptimization::getRegionEndpoints_()</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a5678eb60386afb7f97145b361bd3947f">TwoDOptimization::optimize()</a>, <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_()</a>, and <a class="el" href="classOpenMS_1_1TwoDOptimization.html#adca2617ab638fed2467b9d57b1fe2cfa">TwoDOptimization::optimizeRegionsScanwise_()</a>.</p>
</div>
</div>
<a class="anchor" id="a50d07207174c609658e117b2aa89cb10"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">std::map<<a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a>, std::vector<<a class="el" href="structOpenMS_1_1PeakIndex.html">PeakIndex</a>> > matching_peaks_</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Indices of peaks in the adjacent scans matching peaks in the scan with no. ref_scan. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_()</a>.</p>
</div>
</div>
<a class="anchor" id="a78c0d505b8706df48e8cf696e21035ee"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="group__Concept.html#gaba0996d26f7be2572973245b51852757">UInt</a> max_iteration_</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Convergence Parameter: Maximal number of iterations. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_()</a>.</p>
</div>
</div>
<a class="anchor" id="a58b5225db8586aea7dd011a7447de6af"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> max_peak_distance_</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>upper bound for distance between two peaks belonging to the same region </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a5678eb60386afb7f97145b361bd3947f">TwoDOptimization::optimize()</a>.</p>
</div>
</div>
<a class="anchor" id="a1491750eda19a5fae8d6aa0deafb60ce"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="structOpenMS_1_1OptimizationFunctions_1_1PenaltyFactorsIntensity.html">OptimizationFunctions::PenaltyFactorsIntensity</a> penalties_</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Penalty factors for some parameters in the optimization. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a17e2d6f48048565ca00dee8f87da38ba">TwoDOptimization::optimizeRegions_()</a>.</p>
</div>
</div>
<a class="anchor" id="a5ecbb7085dd05993affbe76a8eae8718"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">bool real_2D_</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Optimization considering all scans of a cluster or optimization of each scan separately. </p>
<p>Referenced by <a class="el" href="classOpenMS_1_1TwoDOptimization.html#a5678eb60386afb7f97145b361bd3947f">TwoDOptimization::optimize()</a>.</p>
</div>
</div>
<a class="anchor" id="acbc4c0b42c88614c321ed3a8e4075c08"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> tolerance_mz_</td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">protected</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>threshold for the difference in the peak position of two matching peaks </p>
</div>
</div>
</div><!-- contents -->
<HR style="height:1px; border:none; border-top:1px solid #c0c0c0;">
<TABLE width="100%" border="0">
<TR>
<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:35 using doxygen 1.8.5</font></TD>
</TR>
</TABLE>
</BODY>
</HTML>
|
