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SuperHirnParameters Class Reference

SuperHirn parameters singleton class containing all static configuration variables. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnParameters.h>

Public Member Functions

 ~SuperHirnParameters ()
 
double getBackgroundIntensityBinsTR ()
 
double getBackgroundIntensityBinsMZ ()
 
double getBackgroundIntensityBinsIntens ()
 
int getBackgroundIntensityBinsMinBinCount ()
 
double getMinTR ()
 
double getMaxTR ()
 
double getMinFeatureMZ ()
 
double getMaxFeatureMZ ()
 
int getMinFeatureChrg ()
 
int getMaxFeatureChrg ()
 
float getIntensityThreshold ()
 
double getToleranceMZ ()
 
double getMaxInterScanRetentionTimeDistance ()
 
int getMinNbClusterMembers ()
 
std::map< int, float > * getScanTRIndex ()
 
double getMS1TRResolution ()
 
bool centroidDataModus ()
 
int getCentroidWindowWidth ()
 
double getDetectableIsotopeFactor ()
 
double getIntensityCV ()
 
double getMassTolPpm ()
 
double getMassTolDa ()
 
double getMinIntensity ()
 
double getIntensityFloor ()
 
double getMzTolPpm ()
 
double getTrTol ()
 
double getPeptideProbabilityThreshold ()
 
bool storeAllLowProbabilityMS2Scans ()
 
bool createFeatureElutionProfiles ()
 
bool ms1FeatureClustering ()
 
double getMs1PeakAreaTrResolution ()
 
double getInitialTrTolerance ()
 
double getMs1FeatureMergingTrTolerance ()
 
double getPercentageIntensityElutionBorderVariation ()
 
double getPpmToleranceForMZClustering ()
 
double getLowIntensityMSSignalThreshold ()
 
bool isInitIsotopeDist ()
 
void setInitIsotopeDist ()
 

Static Public Member Functions

static SuperHirnParametersinstance ()
 

Private Member Functions

 SuperHirnParameters ()
 
 SuperHirnParameters (const SuperHirnParameters &)
 
SuperHirnParametersoperator= (const SuperHirnParameters &)
 

Private Attributes

double backgroundIntensityBinsTR_
 
double backgroundIntensityBinsMZ_
 
double backgroundIntensityBinsIntens_
 
int backgroundIntensityBinsMinBinCount_
 
double minTR_
 
double maxTR_
 
double minFeatureMZ_
 
double maxFeatureMZ_
 
int minFeatureChrg_
 
int maxFeatureChrg_
 
float intensityThreshold_
 
double toleranceMZ_
 
double maxInterScanRetentionTimeDistance_
 
int minNbClusterMembers_
 
std::map< int, floatscanTRIndex_
 
double ms1TRResolution_
 
bool centroidDataModus_
 
int centroidWindowWidth_
 
double detectableIsotopeFactor_
 
double intensityCV_
 
double massTolPpm_
 
double massTolDa_
 
double minIntensity_
 
double intensityFloor_
 
double mzTolPpm_
 
double trTol_
 
double peptideProbabilityThreshold_
 
bool storeAllLowProbabilityMS2Scans_
 
bool createFeatureElutionProfiles_
 
bool ms1FeatureClustering_
 
double ms1PeakAreaTrResolution_
 
double initialTrTolerance_
 
double ms1FeatureMergingTrTolerance_
 
double percentageIntensityElutionBorderVariation_
 
double ppmToleranceForMZClustering_
 
double lowIntensityMSSignalThreshold_
 
bool initIsotopeDist_
 

Static Private Attributes

static SuperHirnParametersinstance_
 
static bool haveInstance_
 

Friends

class FeatureFinderAlgorithmSHCtrl
 

Detailed Description

SuperHirn parameters singleton class containing all static configuration variables.

Constructor & Destructor Documentation

◆ ~SuperHirnParameters()

◆ SuperHirnParameters() [1/2]

SuperHirnParameters ( )
private

◆ SuperHirnParameters() [2/2]

SuperHirnParameters ( const SuperHirnParameters )
inlineprivate

Member Function Documentation

◆ centroidDataModus()

bool centroidDataModus ( )
inline

◆ createFeatureElutionProfiles()

bool createFeatureElutionProfiles ( )
inline

◆ getBackgroundIntensityBinsIntens()

double getBackgroundIntensityBinsIntens ( )
inline

◆ getBackgroundIntensityBinsMinBinCount()

int getBackgroundIntensityBinsMinBinCount ( )
inline

◆ getBackgroundIntensityBinsMZ()

double getBackgroundIntensityBinsMZ ( )
inline

◆ getBackgroundIntensityBinsTR()

double getBackgroundIntensityBinsTR ( )
inline

◆ getCentroidWindowWidth()

int getCentroidWindowWidth ( )
inline

◆ getDetectableIsotopeFactor()

double getDetectableIsotopeFactor ( )
inline

◆ getInitialTrTolerance()

double getInitialTrTolerance ( )
inline

◆ getIntensityCV()

double getIntensityCV ( )
inline

◆ getIntensityFloor()

double getIntensityFloor ( )
inline

◆ getIntensityThreshold()

float getIntensityThreshold ( )
inline

◆ getLowIntensityMSSignalThreshold()

double getLowIntensityMSSignalThreshold ( )
inline

◆ getMassTolDa()

double getMassTolDa ( )
inline

◆ getMassTolPpm()

double getMassTolPpm ( )
inline

◆ getMaxFeatureChrg()

int getMaxFeatureChrg ( )
inline

◆ getMaxFeatureMZ()

double getMaxFeatureMZ ( )
inline

◆ getMaxInterScanRetentionTimeDistance()

double getMaxInterScanRetentionTimeDistance ( )
inline

◆ getMaxTR()

double getMaxTR ( )
inline

◆ getMinFeatureChrg()

int getMinFeatureChrg ( )
inline

◆ getMinFeatureMZ()

double getMinFeatureMZ ( )
inline

◆ getMinIntensity()

double getMinIntensity ( )
inline

◆ getMinNbClusterMembers()

int getMinNbClusterMembers ( )
inline

◆ getMinTR()

double getMinTR ( )
inline

◆ getMs1FeatureMergingTrTolerance()

double getMs1FeatureMergingTrTolerance ( )
inline

◆ getMs1PeakAreaTrResolution()

double getMs1PeakAreaTrResolution ( )
inline

◆ getMS1TRResolution()

double getMS1TRResolution ( )
inline

◆ getMzTolPpm()

double getMzTolPpm ( )
inline

◆ getPeptideProbabilityThreshold()

double getPeptideProbabilityThreshold ( )
inline

◆ getPercentageIntensityElutionBorderVariation()

double getPercentageIntensityElutionBorderVariation ( )
inline

◆ getPpmToleranceForMZClustering()

double getPpmToleranceForMZClustering ( )
inline

◆ getScanTRIndex()

std::map< int, float > * getScanTRIndex ( )
inline

◆ getToleranceMZ()

double getToleranceMZ ( )
inline

◆ getTrTol()

double getTrTol ( )
inline

◆ instance()

SuperHirnParameters * instance ( )
inlinestatic

◆ isInitIsotopeDist()

bool isInitIsotopeDist ( )
inline

◆ ms1FeatureClustering()

bool ms1FeatureClustering ( )
inline

◆ operator=()

SuperHirnParameters & operator= ( const SuperHirnParameters )
inlineprivate

◆ setInitIsotopeDist()

void setInitIsotopeDist ( )
inline

◆ storeAllLowProbabilityMS2Scans()

bool storeAllLowProbabilityMS2Scans ( )
inline

Friends And Related Function Documentation

◆ FeatureFinderAlgorithmSHCtrl

friend class FeatureFinderAlgorithmSHCtrl
friend

Member Data Documentation

◆ backgroundIntensityBinsIntens_

double backgroundIntensityBinsIntens_
private

◆ backgroundIntensityBinsMinBinCount_

int backgroundIntensityBinsMinBinCount_
private

◆ backgroundIntensityBinsMZ_

double backgroundIntensityBinsMZ_
private

◆ backgroundIntensityBinsTR_

double backgroundIntensityBinsTR_
private

◆ centroidDataModus_

bool centroidDataModus_
private

◆ centroidWindowWidth_

int centroidWindowWidth_
private

◆ createFeatureElutionProfiles_

bool createFeatureElutionProfiles_
private

◆ detectableIsotopeFactor_

double detectableIsotopeFactor_
private

◆ haveInstance_

bool haveInstance_
staticprivate

◆ initialTrTolerance_

double initialTrTolerance_
private

◆ initIsotopeDist_

bool initIsotopeDist_
private

◆ instance_

SuperHirnParameters* instance_
staticprivate

◆ intensityCV_

double intensityCV_
private

◆ intensityFloor_

double intensityFloor_
private

◆ intensityThreshold_

float intensityThreshold_
private

◆ lowIntensityMSSignalThreshold_

double lowIntensityMSSignalThreshold_
private

◆ massTolDa_

double massTolDa_
private

◆ massTolPpm_

double massTolPpm_
private

◆ maxFeatureChrg_

int maxFeatureChrg_
private

◆ maxFeatureMZ_

double maxFeatureMZ_
private

◆ maxInterScanRetentionTimeDistance_

double maxInterScanRetentionTimeDistance_
private

◆ maxTR_

double maxTR_
private

◆ minFeatureChrg_

int minFeatureChrg_
private

◆ minFeatureMZ_

double minFeatureMZ_
private

◆ minIntensity_

double minIntensity_
private

◆ minNbClusterMembers_

int minNbClusterMembers_
private

◆ minTR_

double minTR_
private

◆ ms1FeatureClustering_

bool ms1FeatureClustering_
private

◆ ms1FeatureMergingTrTolerance_

double ms1FeatureMergingTrTolerance_
private

◆ ms1PeakAreaTrResolution_

double ms1PeakAreaTrResolution_
private

◆ ms1TRResolution_

double ms1TRResolution_
private

◆ mzTolPpm_

double mzTolPpm_
private

◆ peptideProbabilityThreshold_

double peptideProbabilityThreshold_
private

◆ percentageIntensityElutionBorderVariation_

double percentageIntensityElutionBorderVariation_
private

◆ ppmToleranceForMZClustering_

double ppmToleranceForMZClustering_
private

◆ scanTRIndex_

std::map<int, float> scanTRIndex_
private

◆ storeAllLowProbabilityMS2Scans_

bool storeAllLowProbabilityMS2Scans_
private

◆ toleranceMZ_

double toleranceMZ_
private

◆ trTol_

double trTol_
private

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:13 using doxygen 1.8.13