| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | Static Private Attributes | Friends | List of all members
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 SuperHirnParameters * | instance ()

## Private Member Functions

| SuperHirnParameters ()
| SuperHirnParameters (const SuperHirnParameters &)
SuperHirnParameters & | operator= (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, float > | scanTRIndex_
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 SuperHirnParameters * | instance_
static bool | haveInstance_

## Friends

class | FeatureFinderAlgorithmSHCtrl

## Detailed Description

SuperHirn parameters singleton class containing all static configuration variables.

## Constructor & Destructor Documentation

## ◆ ~SuperHirnParameters()

~SuperHirnParameters | ( |  | ) |

## ◆ SuperHirnParameters() [1/2]

SuperHirnParameters | ( |  | ) |

private

Referenced by SuperHirnParameters::instance().

## ◆ SuperHirnParameters() [2/2]

SuperHirnParameters | ( | const SuperHirnParameters & |  | ) |

inline private

## Member Function Documentation

## ◆ centroidDataModus()

bool centroidDataModus | ( |  | ) |

inline

References SuperHirnParameters::centroidDataModus_.

## ◆ createFeatureElutionProfiles()

bool createFeatureElutionProfiles | ( |  | ) |

inline

References SuperHirnParameters::createFeatureElutionProfiles_.

## ◆ getBackgroundIntensityBinsIntens()

double getBackgroundIntensityBinsIntens | ( |  | ) |

inline

References SuperHirnParameters::backgroundIntensityBinsIntens_.

## ◆ getBackgroundIntensityBinsMinBinCount()

int getBackgroundIntensityBinsMinBinCount | ( |  | ) |

inline

References SuperHirnParameters::backgroundIntensityBinsMinBinCount_.

## ◆ getBackgroundIntensityBinsMZ()

double getBackgroundIntensityBinsMZ | ( |  | ) |

inline

References SuperHirnParameters::backgroundIntensityBinsMZ_.

## ◆ getBackgroundIntensityBinsTR()

double getBackgroundIntensityBinsTR | ( |  | ) |

inline

References SuperHirnParameters::backgroundIntensityBinsTR_.

## ◆ getCentroidWindowWidth()

int getCentroidWindowWidth | ( |  | ) |

inline

References SuperHirnParameters::centroidWindowWidth_.

## ◆ getDetectableIsotopeFactor()

double getDetectableIsotopeFactor | ( |  | ) |

inline

References SuperHirnParameters::detectableIsotopeFactor_.

## ◆ getInitialTrTolerance()

double getInitialTrTolerance | ( |  | ) |

inline

References SuperHirnParameters::initialTrTolerance_.

## ◆ getIntensityCV()

double getIntensityCV | ( |  | ) |

inline

References SuperHirnParameters::intensityCV_.

## ◆ getIntensityFloor()

double getIntensityFloor | ( |  | ) |

inline

References SuperHirnParameters::intensityFloor_.

## ◆ getIntensityThreshold()

float getIntensityThreshold | ( |  | ) |

inline

References SuperHirnParameters::intensityThreshold_.

## ◆ getLowIntensityMSSignalThreshold()

double getLowIntensityMSSignalThreshold | ( |  | ) |

inline

References SuperHirnParameters::lowIntensityMSSignalThreshold_.

## ◆ getMassTolDa()

double getMassTolDa | ( |  | ) |

inline

References SuperHirnParameters::massTolDa_.

## ◆ getMassTolPpm()

double getMassTolPpm | ( |  | ) |

inline

References SuperHirnParameters::massTolPpm_.

## ◆ getMaxFeatureChrg()

int getMaxFeatureChrg | ( |  | ) |

inline

References SuperHirnParameters::maxFeatureChrg_.

## ◆ getMaxFeatureMZ()

double getMaxFeatureMZ | ( |  | ) |

inline

References SuperHirnParameters::maxFeatureMZ_.

## ◆ getMaxInterScanRetentionTimeDistance()

double getMaxInterScanRetentionTimeDistance | ( |  | ) |

inline

References SuperHirnParameters::maxInterScanRetentionTimeDistance_.

## ◆ getMaxTR()

double getMaxTR | ( |  | ) |

inline

References SuperHirnParameters::maxTR_.

## ◆ getMinFeatureChrg()

int getMinFeatureChrg | ( |  | ) |

inline

References SuperHirnParameters::minFeatureChrg_.

## ◆ getMinFeatureMZ()

double getMinFeatureMZ | ( |  | ) |

inline

References SuperHirnParameters::minFeatureMZ_.

## ◆ getMinIntensity()

double getMinIntensity | ( |  | ) |

inline

References SuperHirnParameters::minIntensity_.

## ◆ getMinNbClusterMembers()

int getMinNbClusterMembers | ( |  | ) |

inline

References SuperHirnParameters::minNbClusterMembers_.

## ◆ getMinTR()

double getMinTR | ( |  | ) |

inline

References SuperHirnParameters::minTR_.

## ◆ getMs1FeatureMergingTrTolerance()

double getMs1FeatureMergingTrTolerance | ( |  | ) |

inline

References SuperHirnParameters::ms1FeatureMergingTrTolerance_.

## ◆ getMs1PeakAreaTrResolution()

double getMs1PeakAreaTrResolution | ( |  | ) |

inline

References SuperHirnParameters::ms1PeakAreaTrResolution_.

## ◆ getMS1TRResolution()

double getMS1TRResolution | ( |  | ) |

inline

References SuperHirnParameters::ms1TRResolution_.

## ◆ getMzTolPpm()

double getMzTolPpm | ( |  | ) |

inline

References SuperHirnParameters::mzTolPpm_.

## ◆ getPeptideProbabilityThreshold()

double getPeptideProbabilityThreshold | ( |  | ) |

inline

References SuperHirnParameters::peptideProbabilityThreshold_.

## ◆ getPercentageIntensityElutionBorderVariation()

double getPercentageIntensityElutionBorderVariation | ( |  | ) |

inline

References SuperHirnParameters::percentageIntensityElutionBorderVariation_.

## ◆ getPpmToleranceForMZClustering()

double getPpmToleranceForMZClustering | ( |  | ) |

inline

References SuperHirnParameters::ppmToleranceForMZClustering_.

## ◆ getScanTRIndex()

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

inline

References SuperHirnParameters::scanTRIndex_.

## ◆ getToleranceMZ()

double getToleranceMZ | ( |  | ) |

inline

References SuperHirnParameters::toleranceMZ_.

## ◆ getTrTol()

double getTrTol | ( |  | ) |

inline

References SuperHirnParameters::trTol_.

## ◆ instance()

SuperHirnParameters * instance | ( |  | ) |

inline static

References SuperHirnParameters::haveInstance_, SuperHirnParameters::instance_, and SuperHirnParameters::SuperHirnParameters().

## ◆ isInitIsotopeDist()

bool isInitIsotopeDist | ( |  | ) |

inline

References SuperHirnParameters::initIsotopeDist_.

## ◆ ms1FeatureClustering()

bool ms1FeatureClustering | ( |  | ) |

inline

References SuperHirnParameters::ms1FeatureClustering_.

## ◆ operator=()

SuperHirnParameters & operator= | ( | const SuperHirnParameters & |  | ) |

inline private

## ◆ setInitIsotopeDist()

void setInitIsotopeDist | ( |  | ) |

inline

References SuperHirnParameters::initIsotopeDist_.

## ◆ storeAllLowProbabilityMS2Scans()

bool storeAllLowProbabilityMS2Scans | ( |  | ) |

inline

References SuperHirnParameters::storeAllLowProbabilityMS2Scans_.

## Friends And Related Function Documentation

## ◆ FeatureFinderAlgorithmSHCtrl

friend class FeatureFinderAlgorithmSHCtrl

friend

## Member Data Documentation

## ◆ backgroundIntensityBinsIntens_

double backgroundIntensityBinsIntens_

private

Referenced by SuperHirnParameters::getBackgroundIntensityBinsIntens().

## ◆ backgroundIntensityBinsMinBinCount_

int backgroundIntensityBinsMinBinCount_

private

Referenced by SuperHirnParameters::getBackgroundIntensityBinsMinBinCount().

## ◆ backgroundIntensityBinsMZ_

double backgroundIntensityBinsMZ_

private

Referenced by SuperHirnParameters::getBackgroundIntensityBinsMZ().

## ◆ backgroundIntensityBinsTR_

double backgroundIntensityBinsTR_

private

Referenced by SuperHirnParameters::getBackgroundIntensityBinsTR().

## ◆ centroidDataModus_

bool centroidDataModus_

private

Referenced by SuperHirnParameters::centroidDataModus().

## ◆ centroidWindowWidth_

int centroidWindowWidth_

private

Referenced by SuperHirnParameters::getCentroidWindowWidth().

## ◆ createFeatureElutionProfiles_

bool createFeatureElutionProfiles_

private

Referenced by SuperHirnParameters::createFeatureElutionProfiles().

## ◆ detectableIsotopeFactor_

double detectableIsotopeFactor_

private

Referenced by SuperHirnParameters::getDetectableIsotopeFactor().

## ◆ haveInstance_

bool haveInstance_

static private

Referenced by SuperHirnParameters::instance().

## ◆ initialTrTolerance_

double initialTrTolerance_

private

Referenced by SuperHirnParameters::getInitialTrTolerance().

## ◆ initIsotopeDist_

bool initIsotopeDist_

private

Referenced by SuperHirnParameters::isInitIsotopeDist(), and SuperHirnParameters::setInitIsotopeDist().

## ◆ instance_

SuperHirnParameters* instance_

static private

Referenced by SuperHirnParameters::instance().

## ◆ intensityCV_

double intensityCV_

private

Referenced by SuperHirnParameters::getIntensityCV().

## ◆ intensityFloor_

double intensityFloor_

private

Referenced by SuperHirnParameters::getIntensityFloor().

## ◆ intensityThreshold_

float intensityThreshold_

private

Referenced by SuperHirnParameters::getIntensityThreshold().

## ◆ lowIntensityMSSignalThreshold_

double lowIntensityMSSignalThreshold_

private

Referenced by SuperHirnParameters::getLowIntensityMSSignalThreshold().

## ◆ massTolDa_

double massTolDa_

private

Referenced by SuperHirnParameters::getMassTolDa().

## ◆ massTolPpm_

double massTolPpm_

private

Referenced by SuperHirnParameters::getMassTolPpm().

## ◆ maxFeatureChrg_

int maxFeatureChrg_

private

Referenced by SuperHirnParameters::getMaxFeatureChrg().

## ◆ maxFeatureMZ_

double maxFeatureMZ_

private

Referenced by SuperHirnParameters::getMaxFeatureMZ().

## ◆ maxInterScanRetentionTimeDistance_

double maxInterScanRetentionTimeDistance_

private

Referenced by SuperHirnParameters::getMaxInterScanRetentionTimeDistance().

## ◆ maxTR_

double maxTR_

private

Referenced by SuperHirnParameters::getMaxTR().

## ◆ minFeatureChrg_

int minFeatureChrg_

private

Referenced by SuperHirnParameters::getMinFeatureChrg().

## ◆ minFeatureMZ_

double minFeatureMZ_

private

Referenced by SuperHirnParameters::getMinFeatureMZ().

## ◆ minIntensity_

double minIntensity_

private

Referenced by SuperHirnParameters::getMinIntensity().

## ◆ minNbClusterMembers_

int minNbClusterMembers_

private

Referenced by SuperHirnParameters::getMinNbClusterMembers().

## ◆ minTR_

double minTR_

private

Referenced by SuperHirnParameters::getMinTR().

## ◆ ms1FeatureClustering_

bool ms1FeatureClustering_

private

Referenced by SuperHirnParameters::ms1FeatureClustering().

## ◆ ms1FeatureMergingTrTolerance_

double ms1FeatureMergingTrTolerance_

private

Referenced by SuperHirnParameters::getMs1FeatureMergingTrTolerance().

## ◆ ms1PeakAreaTrResolution_

double ms1PeakAreaTrResolution_

private

Referenced by SuperHirnParameters::getMs1PeakAreaTrResolution().

## ◆ ms1TRResolution_

double ms1TRResolution_

private

Referenced by SuperHirnParameters::getMS1TRResolution().

## ◆ mzTolPpm_

double mzTolPpm_

private

Referenced by SuperHirnParameters::getMzTolPpm().

## ◆ peptideProbabilityThreshold_

double peptideProbabilityThreshold_

private

Referenced by SuperHirnParameters::getPeptideProbabilityThreshold().

## ◆ percentageIntensityElutionBorderVariation_

double percentageIntensityElutionBorderVariation_

private

Referenced by SuperHirnParameters::getPercentageIntensityElutionBorderVariation().

## ◆ ppmToleranceForMZClustering_

double ppmToleranceForMZClustering_

private

Referenced by SuperHirnParameters::getPpmToleranceForMZClustering().

## ◆ scanTRIndex_

std::map<int, float> scanTRIndex_

private

Referenced by SuperHirnParameters::getScanTRIndex().

## ◆ storeAllLowProbabilityMS2Scans_

bool storeAllLowProbabilityMS2Scans_

private

Referenced by SuperHirnParameters::storeAllLowProbabilityMS2Scans().

## ◆ toleranceMZ_

double toleranceMZ_

private

Referenced by SuperHirnParameters::getToleranceMZ().

## ◆ trTol_

double trTol_

private

Referenced by SuperHirnParameters::getTrTol().