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 &  )

inlineprivate

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 ( )

inlinestatic

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 &  )

inlineprivate

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_

staticprivate

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_

staticprivate

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().