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SuperHirnParameters.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Peter Kunszt $
32 // $Authors: Peter Kunszt $
33 // --------------------------------------------------------------------------
34 //
35
36 #pragma once
37
38 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.h>
39
40 namespace OpenMS
41 {
42
47 class SuperHirnParameters
48 {
49 public:
50 static SuperHirnParameters * instance();
51
52 ~SuperHirnParameters();
53
54 double getBackgroundIntensityBinsTR();
55 double getBackgroundIntensityBinsMZ();
56 double getBackgroundIntensityBinsIntens();
57 int getBackgroundIntensityBinsMinBinCount();
58
59 double getMinTR();
60 double getMaxTR();
61 double getMinFeatureMZ();
62 double getMaxFeatureMZ();
63 int getMinFeatureChrg();
64 int getMaxFeatureChrg();
65
66 float getIntensityThreshold();
67 double getToleranceMZ();
68 double getMaxInterScanRetentionTimeDistance();
69 int getMinNbClusterMembers();
70 std::map<int, float> * getScanTRIndex();
71 // bool getMonoIsoDebugging();
72 // double getDebugMonoIsoMassMin();
73 // double getDebugMonoIsoMassMax();
74 // double getMS1IntensityApexPercentilCutoff();
75 double getMS1TRResolution();
76 bool centroidDataModus();
77 int getCentroidWindowWidth();
78
79 double getDetectableIsotopeFactor();
80 /*
81 * @brief Maximal deviation between expected and measured isotopic intensities
82 */
83 double getIntensityCV();
84
85 /*
86 * @brief Mass tolerance in ppm between isotopes
87 */
88 double getMassTolPpm();
89
90 /*
91 * @brief Mass tolerance in Da between isotopes - total mass to = mass*fMassTolPpm/1000000 + fMassTolDa
92 */
93 double getMassTolDa();
94
95 /*
96 * @brief Peak below this values are not considered as monoisotopic peaks
97 */
98 double getMinIntensity();
99
100 /*
101 * @brief Intensities below this value are considered as 0
102 */
103 double getIntensityFloor();
104
105 /*
106 * @brief M/Z tolerance in Parts per Million
107 */
108 double getMzTolPpm();
109
110 /*
111 * @brief TR tolerance
112 */
113 double getTrTol();
114
115 double getPeptideProbabilityThreshold();
116 bool storeAllLowProbabilityMS2Scans();
117
118 bool createFeatureElutionProfiles();
119 bool ms1FeatureClustering();
120
121 double getMs1PeakAreaTrResolution();
122 double getInitialTrTolerance();
123 double getMs1FeatureMergingTrTolerance();
124 double getPercentageIntensityElutionBorderVariation();
125 double getPpmToleranceForMZClustering();
126
127 double getLowIntensityMSSignalThreshold();
128
129 bool isInitIsotopeDist();
130 void setInitIsotopeDist();
131
132 friend class FeatureFinderAlgorithmSHCtrl;
133
134 private:
135 /*
136 * @brief The constructors are private as only the class itself
137 * can construct an instance. Use the static instance() method to access the parameters.
138 */
139 SuperHirnParameters();
140 SuperHirnParameters(const SuperHirnParameters &);
141 SuperHirnParameters & operator=(const SuperHirnParameters &);
142
143 static SuperHirnParameters * instance_; // the singleton instance
144 static bool haveInstance_;
145
146 double backgroundIntensityBinsTR_;
147 double backgroundIntensityBinsMZ_;
148 double backgroundIntensityBinsIntens_;
149 int backgroundIntensityBinsMinBinCount_;
150
151 double minTR_;
152 double maxTR_;
153 double minFeatureMZ_;
154 double maxFeatureMZ_;
155 int minFeatureChrg_;
156 int maxFeatureChrg_;
157
158 float intensityThreshold_; // minimal intensity level: NEVER USED
159 double toleranceMZ_; // m/z tolerance value: NEVER CONFIGURED
160 double maxInterScanRetentionTimeDistance_; // max_distance from next elution peak member in min.
161 int minNbClusterMembers_; // define minimal number of members in LC elution peaks cluster
162
163 std::map<int, float> scanTRIndex_;
164
165 // bool monoIsoDebugging_; // to track detected monoisotopic mass for debugging
166 // double debugMonoIsoMassMin_;
167 // double debugMonoIsoMassMax_;
168 // double ms1IntensityApexPercentilCutoff_;
169 double ms1TRResolution_;
170 bool centroidDataModus_; // if data are in centroid form or not
171 int centroidWindowWidth_;
172
173 // int reportMonoPeaks_; // 1 if info about monoisotopic peaks should be written to mono_peaks.txt
174 // std::string debugDirectory_; // Directory where peak detection debug files are written
175 // int reportScanNumber_; // if sfReportMonoPeaks is set to 1, details about this spectrum will be written to debug files
176
177 // int ms1BaseInterScanDistance_;
178 // int ms2BaseInterScanDistance;
179 // bool ms2PeakProcessing_;
180
181 // std::vector<double> peakExtractionScanLevels_;
182 // std::vector<double> fragmentMassScanLevels_;
183
184 double detectableIsotopeFactor_;
185 double intensityCV_;
186
187 double massTolPpm_; // mass tolerance in ppm between isotopes
188 double massTolDa_; // mass tolerance in Da between isotopes - total mass to = mass*fMassTolPpm/1000000 + fMassTolDa
189 double minIntensity_; // peak below this values are not considered as monoisotopic peaks
190 double intensityFloor_; // intensities below this value are considered as 0
191
192
193 double mzTolPpm_; // tolerance in m/z and TR:
194 double trTol_;
195 double peptideProbabilityThreshold_;
196 bool storeAllLowProbabilityMS2Scans_;
197
198 bool createFeatureElutionProfiles_;
199 bool ms1FeatureClustering_;
200
201 double ms1PeakAreaTrResolution_;
202 double initialTrTolerance_;
203 double ms1FeatureMergingTrTolerance_;
204 double percentageIntensityElutionBorderVariation_;
205 double ppmToleranceForMZClustering_;
206
207 double lowIntensityMSSignalThreshold_;
208 bool initIsotopeDist_;
209
210 };
211
212 //------------------------- inline methods --------------------------
213
214 inline SuperHirnParameters::SuperHirnParameters(const SuperHirnParameters &)
215 {
216 }
217
218 inline SuperHirnParameters & SuperHirnParameters::operator=(const SuperHirnParameters &)
219 {
220 return *this;
221 }
222
223 inline SuperHirnParameters * SuperHirnParameters::instance()
224 {
225 if (haveInstance_)
226 {
227 return instance_;
228 }
229 instance_ = new SuperHirnParameters();
230 haveInstance_ = true;
231 return instance_;
232 }
233
234 inline double SuperHirnParameters::getBackgroundIntensityBinsTR()
235 {
236 return backgroundIntensityBinsTR_;
237 }
238
239 inline double SuperHirnParameters::getBackgroundIntensityBinsMZ()
240 {
241 return backgroundIntensityBinsMZ_;
242 }
243
244 inline double SuperHirnParameters::getBackgroundIntensityBinsIntens()
245 {
246 return backgroundIntensityBinsIntens_;
247 }
248
249 inline int SuperHirnParameters::getBackgroundIntensityBinsMinBinCount()
250 {
251 return backgroundIntensityBinsMinBinCount_;
252 }
253
254 inline double SuperHirnParameters::getMinTR()
255 {
256 return minTR_;
257 }
258
259 inline double SuperHirnParameters::getMaxTR()
260 {
261 return maxTR_;
262 }
263
264 inline double SuperHirnParameters::getMinFeatureMZ()
265 {
266 return minFeatureMZ_;
267 }
268
269 inline double SuperHirnParameters::getMaxFeatureMZ()
270 {
271 return maxFeatureMZ_;
272 }
273
274 inline int SuperHirnParameters::getMinFeatureChrg()
275 {
276 return minFeatureChrg_;
277 }
278
279 inline int SuperHirnParameters::getMaxFeatureChrg()
280 {
281 return maxFeatureChrg_;
282 }
283
284 inline float SuperHirnParameters::getIntensityThreshold()
285 {
286 return intensityThreshold_;
287 }
288
289 inline double SuperHirnParameters::getToleranceMZ()
290 {
291 return toleranceMZ_;
292 }
293
294 inline double SuperHirnParameters::getMaxInterScanRetentionTimeDistance()
295 {
296 return maxInterScanRetentionTimeDistance_;
297 }
298
299 inline int SuperHirnParameters::getMinNbClusterMembers()
300 {
301 return minNbClusterMembers_;
302 }
303
304 inline std::map<int, float> * SuperHirnParameters::getScanTRIndex()
305 {
306 return &scanTRIndex_;
307 }
308
309 /*
310 inline bool SuperHirnParameters::getMonoIsoDebugging()
311 {
312 return monoIsoDebugging_;
313 }
314
315 inline double SuperHirnParameters::getDebugMonoIsoMassMin()
316 {
317 return debugMonoIsoMassMin_;
318 }
319
320 inline double SuperHirnParameters::getDebugMonoIsoMassMax()
321 {
322 return debugMonoIsoMassMax_;
323 }
324
325 inline double SuperHirnParameters::getMS1IntensityApexPercentilCutoff()
326 {
327 return ms1IntensityApexPercentilCutoff_;
328 }
329 */
330
331 inline double SuperHirnParameters::getMS1TRResolution()
332 {
333 return ms1TRResolution_;
334 }
335
336 inline bool SuperHirnParameters::centroidDataModus()
337 {
338 return centroidDataModus_;
339 }
340
341 inline int SuperHirnParameters::getCentroidWindowWidth()
342 {
343 return centroidWindowWidth_;
344 }
345
346 inline double SuperHirnParameters::getDetectableIsotopeFactor()
347 {
348 return detectableIsotopeFactor_;
349 }
350
351 inline double SuperHirnParameters::getIntensityCV()
352 {
353 return intensityCV_;
354 }
355
356 inline double SuperHirnParameters::getMassTolPpm()
357 {
358 return massTolPpm_;
359 }
360
361 inline double SuperHirnParameters::getMassTolDa()
362 {
363 return massTolDa_;
364 }
365
366 inline double SuperHirnParameters::getMinIntensity()
367 {
368 return minIntensity_;
369 }
370
371 inline double SuperHirnParameters::getIntensityFloor()
372 {
373 return intensityFloor_;
374 }
375
376 inline double SuperHirnParameters::getMzTolPpm()
377 {
378 return mzTolPpm_;
379 }
380
381 inline double SuperHirnParameters::getTrTol()
382 {
383 return trTol_;
384 }
385
386 inline double SuperHirnParameters::getPeptideProbabilityThreshold()
387 {
388 return peptideProbabilityThreshold_;
389 }
390
391 inline bool SuperHirnParameters::storeAllLowProbabilityMS2Scans()
392 {
393 return storeAllLowProbabilityMS2Scans_;
394 }
395
396 inline bool SuperHirnParameters::createFeatureElutionProfiles()
397 {
398 return createFeatureElutionProfiles_;
399 }
400
401 inline bool SuperHirnParameters::ms1FeatureClustering()
402 {
403 return ms1FeatureClustering_;
404 }
405
406 inline bool SuperHirnParameters::isInitIsotopeDist()
407 {
408 return initIsotopeDist_;
409 }
410
411 inline void SuperHirnParameters::setInitIsotopeDist()
412 {
413 initIsotopeDist_ = true;
414 }
415
416 inline double SuperHirnParameters::getMs1PeakAreaTrResolution()
417 {
418 return ms1PeakAreaTrResolution_;
419 }
420
421 inline double SuperHirnParameters::getInitialTrTolerance()
422 {
423 return initialTrTolerance_;
424 }
425
426 inline double SuperHirnParameters::getMs1FeatureMergingTrTolerance()
427 {
428 return ms1FeatureMergingTrTolerance_;
429 }
430
431 inline double SuperHirnParameters::getPercentageIntensityElutionBorderVariation()
432 {
433 return percentageIntensityElutionBorderVariation_;
434 }
435
436 inline double SuperHirnParameters::getPpmToleranceForMZClustering()
437 {
438 return ppmToleranceForMZClustering_;
439 }
440
441 inline double SuperHirnParameters::getLowIntensityMSSignalThreshold()
442 {
443 return lowIntensityMSSignalThreshold_;
444 }
445
446 }
447
OpenMS::SuperHirnParameters::getMzTolPpm
double getMzTolPpm()
Definition: SuperHirnParameters.h:376
OpenMS::SuperHirnParameters::maxInterScanRetentionTimeDistance_
double maxInterScanRetentionTimeDistance_
Definition: SuperHirnParameters.h:160
OpenMS::SuperHirnParameters::getMinFeatureMZ
double getMinFeatureMZ()
Definition: SuperHirnParameters.h:264
OpenMS::SuperHirnParameters::getMaxTR
double getMaxTR()
Definition: SuperHirnParameters.h:259
OpenMS::SuperHirnParameters::centroidDataModus
bool centroidDataModus()
Definition: SuperHirnParameters.h:336
OpenMS::SuperHirnParameters::instance
static SuperHirnParameters * instance()
Definition: SuperHirnParameters.h:223
OpenMS::SuperHirnParameters::intensityCV_
double intensityCV_
Definition: SuperHirnParameters.h:185
OpenMS::SuperHirnParameters::ppmToleranceForMZClustering_
double ppmToleranceForMZClustering_
Definition: SuperHirnParameters.h:205
OpenMS::SuperHirnParameters::getBackgroundIntensityBinsMinBinCount
int getBackgroundIntensityBinsMinBinCount()
Definition: SuperHirnParameters.h:249
OpenMS::SuperHirnParameters::backgroundIntensityBinsMinBinCount_
int backgroundIntensityBinsMinBinCount_
Definition: SuperHirnParameters.h:149
OpenMS::SuperHirnParameters::backgroundIntensityBinsIntens_
double backgroundIntensityBinsIntens_
Definition: SuperHirnParameters.h:148
OpenMS::SuperHirnParameters::operator=
SuperHirnParameters & operator=(const SuperHirnParameters &)
Definition: SuperHirnParameters.h:218
OpenMS::SuperHirnParameters::getInitialTrTolerance
double getInitialTrTolerance()
Definition: SuperHirnParameters.h:421
OpenMS::SuperHirnParameters::maxFeatureChrg_
int maxFeatureChrg_
Definition: SuperHirnParameters.h:156
OpenMS::SuperHirnParameters::massTolPpm_
double massTolPpm_
Definition: SuperHirnParameters.h:187
OpenMS::SuperHirnParameters::getPeptideProbabilityThreshold
double getPeptideProbabilityThreshold()
Definition: SuperHirnParameters.h:386
OpenMS::SuperHirnParameters::getMinTR
double getMinTR()
Definition: SuperHirnParameters.h:254
OpenMS::SuperHirnParameters::initIsotopeDist_
bool initIsotopeDist_
Definition: SuperHirnParameters.h:208
OpenMS::SuperHirnParameters::getMinIntensity
double getMinIntensity()
Definition: SuperHirnParameters.h:366
OpenMS::SuperHirnParameters::getMs1FeatureMergingTrTolerance
double getMs1FeatureMergingTrTolerance()
Definition: SuperHirnParameters.h:426
OpenMS::SuperHirnParameters::peptideProbabilityThreshold_
double peptideProbabilityThreshold_
Definition: SuperHirnParameters.h:195
OpenMS::SuperHirnParameters::getTrTol
double getTrTol()
Definition: SuperHirnParameters.h:381
OpenMS::SuperHirnParameters::centroidWindowWidth_
int centroidWindowWidth_
Definition: SuperHirnParameters.h:171
OpenMS::SuperHirnParameters::maxTR_
double maxTR_
Definition: SuperHirnParameters.h:152
OpenMS::SuperHirnParameters::backgroundIntensityBinsTR_
double backgroundIntensityBinsTR_
Definition: SuperHirnParameters.h:146
OpenMS::SuperHirnParameters::toleranceMZ_
double toleranceMZ_
Definition: SuperHirnParameters.h:159
OpenMS::SuperHirnParameters::getPpmToleranceForMZClustering
double getPpmToleranceForMZClustering()
Definition: SuperHirnParameters.h:436
OpenMS::SuperHirnParameters::massTolDa_
double massTolDa_
Definition: SuperHirnParameters.h:188
OpenMS::SuperHirnParameters::lowIntensityMSSignalThreshold_
double lowIntensityMSSignalThreshold_
Definition: SuperHirnParameters.h:207
OpenMS::SuperHirnParameters::centroidDataModus_
bool centroidDataModus_
Definition: SuperHirnParameters.h:170
OpenMS::SuperHirnParameters::setInitIsotopeDist
void setInitIsotopeDist()
Definition: SuperHirnParameters.h:411
OpenMS::SuperHirnParameters::getBackgroundIntensityBinsMZ
double getBackgroundIntensityBinsMZ()
Definition: SuperHirnParameters.h:239
OpenMS::SuperHirnParameters::SuperHirnParameters
SuperHirnParameters()
OpenMS::SuperHirnParameters::getMaxFeatureMZ
double getMaxFeatureMZ()
Definition: SuperHirnParameters.h:269
OpenMS::SuperHirnParameters::getBackgroundIntensityBinsTR
double getBackgroundIntensityBinsTR()
Definition: SuperHirnParameters.h:234
OpenMS::SuperHirnParameters::~SuperHirnParameters
~SuperHirnParameters()
OpenMS::SuperHirnParameters::getIntensityCV
double getIntensityCV()
Definition: SuperHirnParameters.h:351
OpenMS::SuperHirnParameters::getPercentageIntensityElutionBorderVariation
double getPercentageIntensityElutionBorderVariation()
Definition: SuperHirnParameters.h:431
OpenMS::SuperHirnParameters::createFeatureElutionProfiles
bool createFeatureElutionProfiles()
Definition: SuperHirnParameters.h:396
OpenMS::SuperHirnParameters::getLowIntensityMSSignalThreshold
double getLowIntensityMSSignalThreshold()
Definition: SuperHirnParameters.h:441
OpenMS::SuperHirnParameters::mzTolPpm_
double mzTolPpm_
Definition: SuperHirnParameters.h:193
OpenMS::SuperHirnParameters::getIntensityFloor
double getIntensityFloor()
Definition: SuperHirnParameters.h:371
OpenMS::SuperHirnParameters::percentageIntensityElutionBorderVariation_
double percentageIntensityElutionBorderVariation_
Definition: SuperHirnParameters.h:204
OpenMS::SuperHirnParameters::minTR_
double minTR_
Definition: SuperHirnParameters.h:151
OpenMS::SuperHirnParameters::getToleranceMZ
double getToleranceMZ()
Definition: SuperHirnParameters.h:289
OpenMS::SuperHirnParameters::minFeatureChrg_
int minFeatureChrg_
Definition: SuperHirnParameters.h:155
OpenMS::SuperHirnParameters::scanTRIndex_
std::map< int, float > scanTRIndex_
Definition: SuperHirnParameters.h:163
OpenMS::SuperHirnParameters::detectableIsotopeFactor_
double detectableIsotopeFactor_
Definition: SuperHirnParameters.h:184
OpenMS::SuperHirnParameters::getMassTolPpm
double getMassTolPpm()
Definition: SuperHirnParameters.h:356
OpenMS::FeatureFinderAlgorithmSHCtrl
A facade for various Superhirn FeatureFinder classes. Use FeatureFinderAlgorithmSH instead...
Definition: FeatureFinderAlgorithmSHCtrl.h:55
OpenMS::SuperHirnParameters::getBackgroundIntensityBinsIntens
double getBackgroundIntensityBinsIntens()
Definition: SuperHirnParameters.h:244
OpenMS::SuperHirnParameters::minFeatureMZ_
double minFeatureMZ_
Definition: SuperHirnParameters.h:153
OpenMS::SuperHirnParameters::storeAllLowProbabilityMS2Scans_
bool storeAllLowProbabilityMS2Scans_
Definition: SuperHirnParameters.h:196
OpenMS::SuperHirnParameters::ms1FeatureMergingTrTolerance_
double ms1FeatureMergingTrTolerance_
Definition: SuperHirnParameters.h:203
OpenMS::SuperHirnParameters::intensityFloor_
double intensityFloor_
Definition: SuperHirnParameters.h:190
OpenMS::SuperHirnParameters::getDetectableIsotopeFactor
double getDetectableIsotopeFactor()
Definition: SuperHirnParameters.h:346
OpenMS::SuperHirnParameters::getMs1PeakAreaTrResolution
double getMs1PeakAreaTrResolution()
Definition: SuperHirnParameters.h:416
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SuperHirnParameters::createFeatureElutionProfiles_
bool createFeatureElutionProfiles_
Definition: SuperHirnParameters.h:198
OpenMS::SuperHirnParameters::ms1FeatureClustering_
bool ms1FeatureClustering_
Definition: SuperHirnParameters.h:199
OpenMS::SuperHirnParameters
SuperHirn parameters singleton class containing all static configuration variables.
Definition: SuperHirnParameters.h:47
OpenMS::SuperHirnParameters::getCentroidWindowWidth
int getCentroidWindowWidth()
Definition: SuperHirnParameters.h:341
OpenMS::SuperHirnParameters::initialTrTolerance_
double initialTrTolerance_
Definition: SuperHirnParameters.h:202
OpenMS::SuperHirnParameters::backgroundIntensityBinsMZ_
double backgroundIntensityBinsMZ_
Definition: SuperHirnParameters.h:147
OpenMS::SuperHirnParameters::getMinNbClusterMembers
int getMinNbClusterMembers()
Definition: SuperHirnParameters.h:299
OpenMS::SuperHirnParameters::trTol_
double trTol_
Definition: SuperHirnParameters.h:194
OpenMS::SuperHirnParameters::minIntensity_
double minIntensity_
Definition: SuperHirnParameters.h:189
OpenMS::SuperHirnParameters::intensityThreshold_
float intensityThreshold_
Definition: SuperHirnParameters.h:158
OpenMS::SuperHirnParameters::isInitIsotopeDist
bool isInitIsotopeDist()
Definition: SuperHirnParameters.h:406
OpenMS::SuperHirnParameters::getMaxInterScanRetentionTimeDistance
double getMaxInterScanRetentionTimeDistance()
Definition: SuperHirnParameters.h:294
OpenMS::SuperHirnParameters::storeAllLowProbabilityMS2Scans
bool storeAllLowProbabilityMS2Scans()
Definition: SuperHirnParameters.h:391
OpenMS::SuperHirnParameters::ms1TRResolution_
double ms1TRResolution_
Definition: SuperHirnParameters.h:169
OpenMS::SuperHirnParameters::minNbClusterMembers_
int minNbClusterMembers_
Definition: SuperHirnParameters.h:161
OpenMS::SuperHirnParameters::getScanTRIndex
std::map< int, float > * getScanTRIndex()
Definition: SuperHirnParameters.h:304
OpenMS::SuperHirnParameters::getMS1TRResolution
double getMS1TRResolution()
Definition: SuperHirnParameters.h:331
OpenMS::SuperHirnParameters::ms1PeakAreaTrResolution_
double ms1PeakAreaTrResolution_
Definition: SuperHirnParameters.h:201
OpenMS::SuperHirnParameters::getIntensityThreshold
float getIntensityThreshold()
Definition: SuperHirnParameters.h:284
OpenMS::SuperHirnParameters::haveInstance_
static bool haveInstance_
Definition: SuperHirnParameters.h:144
OpenMS::SuperHirnParameters::getMassTolDa
double getMassTolDa()
Definition: SuperHirnParameters.h:361
OpenMS::SuperHirnParameters::getMinFeatureChrg
int getMinFeatureChrg()
Definition: SuperHirnParameters.h:274
OpenMS::SuperHirnParameters::maxFeatureMZ_
double maxFeatureMZ_
Definition: SuperHirnParameters.h:154
OpenMS::SuperHirnParameters::ms1FeatureClustering
bool ms1FeatureClustering()
Definition: SuperHirnParameters.h:401
OpenMS::SuperHirnParameters::instance_
static SuperHirnParameters * instance_
Definition: SuperHirnParameters.h:143
OpenMS::SuperHirnParameters::getMaxFeatureChrg
int getMaxFeatureChrg()
Definition: SuperHirnParameters.h:279