SuperHirnParameters Class Reference

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

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

List of all members.

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

(

)

[private]

Referenced by SuperHirnParameters::instance().

SuperHirnParameters

(

const SuperHirnParameters &

)

[inline, private]

---

Member Function Documentation

bool centroidDataModus

(

)

[inline]

References SuperHirnParameters::centroidDataModus_.

bool createFeatureElutionProfiles

(

)

[inline]

References SuperHirnParameters::createFeatureElutionProfiles_.

double getBackgroundIntensityBinsIntens

(

)

[inline]

References SuperHirnParameters::backgroundIntensityBinsIntens_.

int getBackgroundIntensityBinsMinBinCount

(

)

[inline]

References SuperHirnParameters::backgroundIntensityBinsMinBinCount_.

double getBackgroundIntensityBinsMZ

(

)

[inline]

References SuperHirnParameters::backgroundIntensityBinsMZ_.

double getBackgroundIntensityBinsTR

(

)

[inline]

References SuperHirnParameters::backgroundIntensityBinsTR_.

int getCentroidWindowWidth

(

)

[inline]

References SuperHirnParameters::centroidWindowWidth_.

double getDetectableIsotopeFactor

(

)

[inline]

References SuperHirnParameters::detectableIsotopeFactor_.

double getInitialTrTolerance

(

)

[inline]

References SuperHirnParameters::initialTrTolerance_.

double getIntensityCV

(

)

[inline]

References SuperHirnParameters::intensityCV_.

double getIntensityFloor

(

)

[inline]

References SuperHirnParameters::intensityFloor_.

float getIntensityThreshold

(

)

[inline]

References SuperHirnParameters::intensityThreshold_.

Referenced by ProcessData::getMinimalIntensityLevel().

double getLowIntensityMSSignalThreshold

(

)

[inline]

References SuperHirnParameters::lowIntensityMSSignalThreshold_.

double getMassTolDa

(

)

[inline]

References SuperHirnParameters::massTolDa_.

double getMassTolPpm

(

)

[inline]

References SuperHirnParameters::massTolPpm_.

int getMaxFeatureChrg

(

)

[inline]

References SuperHirnParameters::maxFeatureChrg_.

double getMaxFeatureMZ

(

)

[inline]

References SuperHirnParameters::maxFeatureMZ_.

double getMaxInterScanRetentionTimeDistance

(

)

[inline]

References SuperHirnParameters::maxInterScanRetentionTimeDistance_.

double getMaxTR

(

)

[inline]

References SuperHirnParameters::maxTR_.

int getMinFeatureChrg

(

)

[inline]

References SuperHirnParameters::minFeatureChrg_.

double getMinFeatureMZ

(

)

[inline]

References SuperHirnParameters::minFeatureMZ_.

double getMinIntensity

(

)

[inline]

References SuperHirnParameters::minIntensity_.

int getMinNbClusterMembers

(

)

[inline]

References SuperHirnParameters::minNbClusterMembers_.

double getMinTR

(

)

[inline]

References SuperHirnParameters::minTR_.

double getMs1FeatureMergingTrTolerance

(

)

[inline]

References SuperHirnParameters::ms1FeatureMergingTrTolerance_.

double getMs1PeakAreaTrResolution

(

)

[inline]

References SuperHirnParameters::ms1PeakAreaTrResolution_.

double getMS1TRResolution

(

)

[inline]

References SuperHirnParameters::ms1TRResolution_.

double getMzTolPpm

(

)

[inline]

References SuperHirnParameters::mzTolPpm_.

double getPeptideProbabilityThreshold

(

)

[inline]

References SuperHirnParameters::peptideProbabilityThreshold_.

double getPercentageIntensityElutionBorderVariation

(

)

[inline]

References SuperHirnParameters::percentageIntensityElutionBorderVariation_.

double getPpmToleranceForMZClustering

(

)

[inline]

References SuperHirnParameters::ppmToleranceForMZClustering_.

std::map< int, float > * getScanTRIndex

(

)

[inline]

References SuperHirnParameters::scanTRIndex_.

double getToleranceMZ

(

)

[inline]

References SuperHirnParameters::toleranceMZ_.

double getTrTol

(

)

[inline]

References SuperHirnParameters::trTol_.

SuperHirnParameters * instance

(

)

[inline, static]

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

Referenced by ProcessData::getMinimalIntensityLevel().

bool isInitIsotopeDist

(

)

[inline]

References SuperHirnParameters::initIsotopeDist_.

bool ms1FeatureClustering

(

)

[inline]

References SuperHirnParameters::ms1FeatureClustering_.

SuperHirnParameters & operator=

(

const SuperHirnParameters &

)

[inline, private]

void setInitIsotopeDist

(

)

[inline]

References SuperHirnParameters::initIsotopeDist_.

bool storeAllLowProbabilityMS2Scans

(

)

[inline]

References SuperHirnParameters::storeAllLowProbabilityMS2Scans_.

---

Friends And Related Function Documentation

friend class FeatureFinderAlgorithmSHCtrl [friend]

---

Member Data Documentation

double backgroundIntensityBinsIntens_ [private]

Referenced by SuperHirnParameters::getBackgroundIntensityBinsIntens().

int backgroundIntensityBinsMinBinCount_ [private]

Referenced by SuperHirnParameters::getBackgroundIntensityBinsMinBinCount().

double backgroundIntensityBinsMZ_ [private]

Referenced by SuperHirnParameters::getBackgroundIntensityBinsMZ().

double backgroundIntensityBinsTR_ [private]

Referenced by SuperHirnParameters::getBackgroundIntensityBinsTR().

bool centroidDataModus_ [private]

Referenced by SuperHirnParameters::centroidDataModus().

int centroidWindowWidth_ [private]

Referenced by SuperHirnParameters::getCentroidWindowWidth().

bool createFeatureElutionProfiles_ [private]

Referenced by SuperHirnParameters::createFeatureElutionProfiles().

double detectableIsotopeFactor_ [private]

Referenced by SuperHirnParameters::getDetectableIsotopeFactor().

bool haveInstance_ [static, private]

Referenced by SuperHirnParameters::instance().

double initialTrTolerance_ [private]

Referenced by SuperHirnParameters::getInitialTrTolerance().

bool initIsotopeDist_ [private]

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

SuperHirnParameters* instance_ [static, private]

Referenced by SuperHirnParameters::instance().

double intensityCV_ [private]

Referenced by SuperHirnParameters::getIntensityCV().

double intensityFloor_ [private]

Referenced by SuperHirnParameters::getIntensityFloor().

float intensityThreshold_ [private]

Referenced by SuperHirnParameters::getIntensityThreshold().

double lowIntensityMSSignalThreshold_ [private]

Referenced by SuperHirnParameters::getLowIntensityMSSignalThreshold().

double massTolDa_ [private]

Referenced by SuperHirnParameters::getMassTolDa().

double massTolPpm_ [private]

Referenced by SuperHirnParameters::getMassTolPpm().

int maxFeatureChrg_ [private]

Referenced by SuperHirnParameters::getMaxFeatureChrg().

double maxFeatureMZ_ [private]

Referenced by SuperHirnParameters::getMaxFeatureMZ().

double maxInterScanRetentionTimeDistance_ [private]

Referenced by SuperHirnParameters::getMaxInterScanRetentionTimeDistance().

double maxTR_ [private]

Referenced by SuperHirnParameters::getMaxTR().

int minFeatureChrg_ [private]

Referenced by SuperHirnParameters::getMinFeatureChrg().

double minFeatureMZ_ [private]

Referenced by SuperHirnParameters::getMinFeatureMZ().

double minIntensity_ [private]

Referenced by SuperHirnParameters::getMinIntensity().

int minNbClusterMembers_ [private]

Referenced by SuperHirnParameters::getMinNbClusterMembers().

double minTR_ [private]

Referenced by SuperHirnParameters::getMinTR().

bool ms1FeatureClustering_ [private]

Referenced by SuperHirnParameters::ms1FeatureClustering().

double ms1FeatureMergingTrTolerance_ [private]

Referenced by SuperHirnParameters::getMs1FeatureMergingTrTolerance().

double ms1PeakAreaTrResolution_ [private]

Referenced by SuperHirnParameters::getMs1PeakAreaTrResolution().

double ms1TRResolution_ [private]

Referenced by SuperHirnParameters::getMS1TRResolution().

double mzTolPpm_ [private]

Referenced by SuperHirnParameters::getMzTolPpm().

double peptideProbabilityThreshold_ [private]

Referenced by SuperHirnParameters::getPeptideProbabilityThreshold().

double percentageIntensityElutionBorderVariation_ [private]

Referenced by SuperHirnParameters::getPercentageIntensityElutionBorderVariation().

double ppmToleranceForMZClustering_ [private]

Referenced by SuperHirnParameters::getPpmToleranceForMZClustering().

std::map<int, float> scanTRIndex_ [private]

Referenced by SuperHirnParameters::getScanTRIndex().

bool storeAllLowProbabilityMS2Scans_ [private]

Referenced by SuperHirnParameters::storeAllLowProbabilityMS2Scans().

double toleranceMZ_ [private]

Referenced by SuperHirnParameters::getToleranceMZ().

double trTol_ [private]

Referenced by SuperHirnParameters::getTrTol().