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

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:21 using doxygen 1.8.5