Class describing a deconvolved mass. A mass contains multiple (LogMz) peaks of different charges and isotope indices. PeakGroup is the set of such peaks representing a single monoisotopic mass. PeakGroup also contains features that define the quality of it. It is used by setQscore calculation. DeconvolvedSpectrum consists of PeakGroups. More...

#include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>

Collaboration diagram for PeakGroup:

[legend]

Public Types
enum	TargetDecoyType { target = 0 , charge_decoy , noise_decoy , isotope_decoy , non_specific }
	target decoy type of PeakGroup. This specifies if a PeakGroup is a target (0), charge decoy (1), noise decoy (2), or isotope decoy (3). Added non_specific (4) to allow all types in some functions More...

Public Member Functions
	PeakGroup ()=default
	default constructor More...

	PeakGroup (int min_abs_charge, int max_abs_charge, bool is_positive)
	Constructor specifying charge range. More...

	~PeakGroup ()=default
	default destructor More...

	PeakGroup (const PeakGroup &)=default
	copy constructor More...

	PeakGroup (PeakGroup &&other)=default
	move constructor More...

bool	operator< (const PeakGroup &a) const
	comparison operators More...

bool	operator> (const PeakGroup &a) const

bool	operator== (const PeakGroup &a) const

PeakGroup &	operator= (const PeakGroup &t)=default
	assignment operator More...

void	updateMonoMassAndIsotopeIntensities ()
	add monoisotopic indices of peaks by offset and discard negative isotope peaks. Total intensity is also updated More...

int	updateQscore (std::vector< LogMzPeak > &noisy_peaks, const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg, double min_cos, bool is_low_charge, bool is_profile=false, int allowed_iso_error=1)
	Update setQscore. Cosine and SNRs are also updated. More...

std::vector< LogMzPeak >	recruitAllPeaksInSpectrum (const MSSpectrum &spec, double tol, const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg, double mono_mass)
	given a monoisotopic mass, recruit raw peaks from the raw input spectrum and add to this peakGroup. This is a bit time-consuming and is done for only a small number of selected high-quality peakgroups. More...

bool	isSignalMZ (double mz, double tol) const
	determine is an mz is a signal of this peakgroup. Input tol is ppm tolerance (e.g., 10.0 for 10ppm tolerance). Assume logMzPeaks are sorted. More...

void	setScanNumber (int scan_number)
	set scan number More...

void	setChargeIsotopeCosine (int abs_charge, float cos)
	set per abs_charge isotope cosine More...

void	setAbsChargeRange (int min_abs_charge, int max_abs_charge)
	set min_abs_charge and max_abs_charge charge range More...

void	setIsotopeCosine (float cos)
	set isotope cosine score More...

void	setRepAbsCharge (int max_snr_abs_charge)
	set representative max_snr_abs_charge More...

void	setMonoisotopicMass (double mono_mass)
	set monoisotopic mass More...

void	setQscore (double qscore)
	set Q score - for FLASHIda log file parsing More...

void	setChargeScore (float charge_score)
	set charge score - for FLASHIda log file parsing More...

void	setAvgPPMError (float error)
	set average mass ppm error More...

void	setSNR (float snr)
	set SNR manually - for FLASHIda log file parsing More...

void	setChargeSNR (int abs_charge, float c_snr)
	set charge SNR manually - for FLASHIda log file parsing More...

void	setTargeted ()
	set if it is targeted More...

int	getScanNumber () const
	get scan number More...

double	getMonoMass () const
	get monoisotopic mass More...

float	getIntensity () const
	get intensity More...

float	getChargeSNR (int abs_charge) const
	get per abs_charge SNR More...

float	getChargeIsotopeCosine (int abs_charge) const
	get per abs_charge isotope cosine More...

float	getChargeIntensity (int abs_charge) const
	get per abs_charge intenstiy More...

std::tuple< double, double >	getRepMzRange () const
	get mz range that results in max setQscore More...

std::tuple< double, double >	getMzRange (int abs_charge) const
	get mz range of the charge More...

std::tuple< int, int >	getAbsChargeRange () const
	get charge range - the actual charge values More...

const std::vector< float > &	getIsotopeIntensities () const
	get per isotope intensities More...

float	getIsotopeCosine () const
	get isotopic cosine score More...

int	getRepAbsCharge () const
	get representative charge More...

double	getQscore () const
	get Q score More...

double	getQscore2D () const
	get feature Q score More...

float	getSNR () const
	get total SNR More...

float	getChargeScore () const
	get charge score More...

float	getAvgPPMError () const
	get average mass ppm error; More...

float	getAvgDaError () const
	get average mass ppm error; More...

bool	isPositive () const
	get if it is positive mode More...

bool	isTargeted () const
	get if it is targeted More...

PeakGroup::TargetDecoyType	getTargetDecoyType () const
	get the target decoy type of this More...

void	setTargetDecoyType (PeakGroup::TargetDecoyType index)
	for this PeakGroup, specify the target decoy type. More...

float	getQvalue (PeakGroup::TargetDecoyType target_decoy_type=PeakGroup::TargetDecoyType::target) const

void	setQvalue (double q, PeakGroup::TargetDecoyType target_decoy_type)

void	setIsotopeDaDistance (double d)
	set distance between consecutive isotopes More...

double	getIsotopeDaDistance () const
	get distance between consecutive isotopes More...

int	getMinNegativeIsotopeIndex () const
	get minimum neagative isotope index More...

void	setIndex (uint i)
	set index of this peak group More...

void	setQscore2D (double fqscore)
	set Q score 2D More...

void	setFeatureIndex (uint findex)
	set feature index More...

uint	getIndex () const
	get index of this peak group More...

uint	getFeatureIndex () const
	get feature index of this peak group More...

int	getChargeRangeForDL ()

int	getIsotopeRangeForDL ()

float	getBinWidthDL ()

void	calculateDLMatrices (const MSSpectrum &spec, double tol, const PrecalculatedAveragine &avg)
	calculate the matrices for DL training and scoring More...

Matrix< float >	getDLMatrix (int index) const
	get the calcualted DL matrix More...

std::vector< FLASHDeconvHelperStructs::LogMzPeak >::const_iterator	begin () const noexcept
	iterators for the signal LogMz peaks in this PeakGroup More...

std::vector< FLASHDeconvHelperStructs::LogMzPeak >::const_iterator	end () const noexcept

std::vector< FLASHDeconvHelperStructs::LogMzPeak >::iterator	begin () noexcept

std::vector< FLASHDeconvHelperStructs::LogMzPeak >::iterator	end () noexcept

const FLASHDeconvHelperStructs::LogMzPeak &	operator[] (Size i) const

std::vector< FLASHDeconvHelperStructs::LogMzPeak >::const_iterator	getNoisePeakBegin () const noexcept
	iterators for the noisy LogMz peaks in this PeakGroup More...

std::vector< FLASHDeconvHelperStructs::LogMzPeak >::const_iterator	getNoisePeakEnd () const noexcept

std::vector< FLASHDeconvHelperStructs::LogMzPeak >::iterator	getNoisePeakBegin () noexcept

std::vector< FLASHDeconvHelperStructs::LogMzPeak >::iterator	getNoisePeakEnd () noexcept

void	push_back (const FLASHDeconvHelperStructs::LogMzPeak &pg)
	vector operators for the LogMzPeaks in this PeakGroup More...

FLASHDeconvHelperStructs::LogMzPeak &	back ()

Size	size () const noexcept

void	reserve (Size n)

bool	empty () const

void	swap (std::vector< FLASHDeconvHelperStructs::LogMzPeak > &x)

void	sort ()

Private Types
typedef FLASHDeconvHelperStructs::LogMzPeak	LogMzPeak

typedef FLASHDeconvHelperStructs::PrecalculatedAveragine	PrecalculatedAveragine

Private Member Functions
void	updateChargeFitScoreAndChargeIntensities_ (bool is_low_charge)
	update chargefit score and also update per charge intensities here. More...

void	updateAvgPPMError_ ()
	update avg ppm error More...

void	updateAvgDaError_ ()
	update avg Da error More...

float	getAbsPPMError_ (const LogMzPeak &p) const
	get ppm error of a logMzPeak More...

float	getAbsDaError_ (const LogMzPeak &p) const
	get Da error of a logMzPeak from the closest isotope More...

void	updateSNR_ ()
	using signal and total (signal + noise) power, update SNR value More...

void	clear_ ()
	clear peaks More...

void	updatePerChargeInformation_ (const std::vector< LogMzPeak > &noisy_peaks)
	update per charge intensities, noise power, and squared intensities. used for SNR estimation More...

void	updateChargeRange_ (std::vector< LogMzPeak > &noisy_peaks)
	update the charge range using the calculated per charge information More...

void	updatePerChargeCos_ (const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg)
	update per charge cosine values More...

float	getNoisePeakPower_ (const std::vector< LogMzPeak > &noisy_peaks, const std::vector< LogMzPeak > &signal_peaks, const int z) const

Private Attributes
std::vector< Matrix< float > >	dl_matrices_

std::vector< FLASHDeconvHelperStructs::LogMzPeak >	logMzpeaks_
	log Mz peaks More...

std::vector< FLASHDeconvHelperStructs::LogMzPeak >	negative_iso_peaks_
	negative isotope index peaks More...

std::vector< float >	per_charge_sum_signal_squared_
	per charge SNR, isotope cosine, and intensity vectors More...

std::vector< float >	per_charge_noise_pwr_

std::vector< float >	per_charge_cos_

std::vector< float >	per_charge_int_

std::vector< float >	per_charge_snr_

std::vector< float >	per_isotope_int_
	per isotope intensity. More...

int	min_abs_charge_ = 0
	charge range More...

int	max_abs_charge_ = -1

uint	index_ = 0
	peak group index More...

uint	findex_ = 0
	feature index More...

int	scan_number_ = 0
	scan number More...

bool	is_positive_ = false
	is positive or not More...

bool	is_targeted_ = false
	if this peak group has been targeted More...

double	monoisotopic_mass_ = -1.0
	information on the deconvolved mass More...

float	intensity_ = 0

PeakGroup::TargetDecoyType	target_decoy_type_ = target
	index to specify if this peak_group is a target (0), an isotope decoy (1), a noise (2), or a charge decoy (3) More...

int	min_negative_isotope_index_ = -1
	up to which negative isotope index should be considered. By considereing negative istoopes, one can reduce isotope index error. More...

int	charge_range_for_DL_ = 7

float	bin_width_DL_ = 0.25

int	iso_range_for_DL_ = 21

double	iso_da_distance_ = Constants::ISOTOPE_MASSDIFF_55K_U
	distance between consecutive isotopes. Can be different for decoys More...

int	max_snr_abs_charge_ = -1
	scoring variables More...

float	isotope_cosine_score_ = 0

float	charge_score_ = 0

double	qscore_ = .0f

double	qscore2D_ = -1.0f

float	avg_ppm_error_ = 0

float	avg_da_error_ = 0

float	snr_ = 0

std::map< PeakGroup::TargetDecoyType, float >	qvalue_
	q values with different decoy types More...

Detailed Description

Class describing a deconvolved mass. A mass contains multiple (LogMz) peaks of different charges and isotope indices. PeakGroup is the set of such peaks representing a single monoisotopic mass. PeakGroup also contains features that define the quality of it. It is used by setQscore calculation. DeconvolvedSpectrum consists of PeakGroups.

Member Typedef Documentation

◆ LogMzPeak

typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak

private

◆ PrecalculatedAveragine

typedef FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine

private

Member Enumeration Documentation

◆ TargetDecoyType

enum TargetDecoyType

target decoy type of PeakGroup. This specifies if a PeakGroup is a target (0), charge decoy (1), noise decoy (2), or isotope decoy (3). Added non_specific (4) to allow all types in some functions

Enumerator
target
charge_decoy
noise_decoy
isotope_decoy
non_specific

Constructor & Destructor Documentation

◆ PeakGroup() [1/4]

PeakGroup ( )

default

default constructor

◆ PeakGroup() [2/4]

PeakGroup	(	int	min_abs_charge,
		int	max_abs_charge,
		bool	is_positive
	)

explicit

Constructor specifying charge range.

Parameters

min_abs_charge	min Charge
max_abs_charge	max Charge
is_positive	whether MS is positive mode

◆ ~PeakGroup()

~PeakGroup ( )

default

default destructor

◆ PeakGroup() [3/4]

PeakGroup ( const PeakGroup & )

default

copy constructor

◆ PeakGroup() [4/4]

PeakGroup ( PeakGroup && other )

default

move constructor

Member Function Documentation

◆ back()

FLASHDeconvHelperStructs::LogMzPeak& back ( )

◆ begin() [1/2]

std::vector<FLASHDeconvHelperStructs::LogMzPeak>::const_iterator begin ( ) const

noexcept

iterators for the signal LogMz peaks in this PeakGroup

◆ begin() [2/2]

std::vector<FLASHDeconvHelperStructs::LogMzPeak>::iterator begin ( )

noexcept

◆ calculateDLMatrices()

void calculateDLMatrices	(	const MSSpectrum &	spec,
		double	tol,
		const PrecalculatedAveragine &	avg
	)

calculate the matrices for DL training and scoring

Parameters

spec	original raw spectrum
tol	mass tolerance
avg	averagine to normalize the observed isotope pattern

◆ clear_()

void clear_ ( )

private

clear peaks

◆ empty()

bool empty ( ) const

◆ end() [1/2]

std::vector<FLASHDeconvHelperStructs::LogMzPeak>::const_iterator end ( ) const

noexcept

◆ end() [2/2]

std::vector<FLASHDeconvHelperStructs::LogMzPeak>::iterator end ( )

noexcept

◆ getAbsChargeRange()

std::tuple<int, int> getAbsChargeRange ( ) const

get charge range - the actual charge values

◆ getAbsDaError_()

float getAbsDaError_ ( const LogMzPeak & p ) const

private

get Da error of a logMzPeak from the closest isotope

◆ getAbsPPMError_()

float getAbsPPMError_ ( const LogMzPeak & p ) const

private

get ppm error of a logMzPeak

◆ getAvgDaError()

float getAvgDaError ( ) const

get average mass ppm error;

◆ getAvgPPMError()

float getAvgPPMError ( ) const

get average mass ppm error;

◆ getBinWidthDL()

float getBinWidthDL ( )

inline

◆ getChargeIntensity()

float getChargeIntensity ( int abs_charge ) const

get per abs_charge intenstiy

◆ getChargeIsotopeCosine()

float getChargeIsotopeCosine ( int abs_charge ) const

get per abs_charge isotope cosine

◆ getChargeRangeForDL()

int getChargeRangeForDL ( )

inline

◆ getChargeScore()

float getChargeScore ( ) const

get charge score

◆ getChargeSNR()

float getChargeSNR ( int abs_charge ) const

get per abs_charge SNR

◆ getDLMatrix()

Matrix<float> getDLMatrix ( int index ) const

get the calcualted DL matrix

◆ getFeatureIndex()

uint getFeatureIndex ( ) const

get feature index of this peak group

◆ getIndex()

uint getIndex ( ) const

get index of this peak group

◆ getIntensity()

float getIntensity ( ) const

get intensity

◆ getIsotopeCosine()

float getIsotopeCosine ( ) const

get isotopic cosine score

◆ getIsotopeDaDistance()

double getIsotopeDaDistance ( ) const

get distance between consecutive isotopes

◆ getIsotopeIntensities()

const std::vector<float>& getIsotopeIntensities ( ) const

get per isotope intensities

◆ getIsotopeRangeForDL()

int getIsotopeRangeForDL ( )

inline

◆ getMinNegativeIsotopeIndex()

int getMinNegativeIsotopeIndex ( ) const

get minimum neagative isotope index

◆ getMonoMass()

double getMonoMass ( ) const

get monoisotopic mass

◆ getMzRange()

std::tuple<double, double> getMzRange ( int abs_charge ) const

get mz range of the charge

◆ getNoisePeakBegin() [1/2]

std::vector<FLASHDeconvHelperStructs::LogMzPeak>::const_iterator getNoisePeakBegin ( ) const

noexcept

iterators for the noisy LogMz peaks in this PeakGroup

◆ getNoisePeakBegin() [2/2]

std::vector<FLASHDeconvHelperStructs::LogMzPeak>::iterator getNoisePeakBegin ( )

noexcept

◆ getNoisePeakEnd() [1/2]

std::vector<FLASHDeconvHelperStructs::LogMzPeak>::const_iterator getNoisePeakEnd ( ) const

noexcept

◆ getNoisePeakEnd() [2/2]

std::vector<FLASHDeconvHelperStructs::LogMzPeak>::iterator getNoisePeakEnd ( )

noexcept

◆ getNoisePeakPower_()

float getNoisePeakPower_	(	const std::vector< LogMzPeak > &	noisy_peaks,
		const std::vector< LogMzPeak > &	signal_peaks,
		const int	z
	)		const

private

calculate noisy peak power. The goal of this function is to group noisy peaks that are possibly from the same molecule and sum their intensities before calculate power

Parameters

noisy_peaks	noisy peaks to calculate power
signal_peaks	signal peaks - they may make a part of noisy isotopes
z	charge

Returns: calculated noise power

◆ getQscore()

double getQscore ( ) const

get Q score

◆ getQscore2D()

double getQscore2D ( ) const

get feature Q score

◆ getQvalue()

float getQvalue ( PeakGroup::TargetDecoyType target_decoy_type = PeakGroup::TargetDecoyType::target ) const

Get q values for different target_decoy_type. For charge, noise, isotope decoy types, q values corresponding to the type will be returned. For target (default), the final q value is calculated by summing the q values of all decoy types and returned.

Parameters

target_decoy_type This target_decoy_type specifies if a PeakGroup is a target (0), charge decoy (1), noise decoy (2), or isotope decoy (3)

Returns: Q value of the peakGroup

◆ getRepAbsCharge()

int getRepAbsCharge ( ) const

get representative charge

◆ getRepMzRange()

std::tuple<double, double> getRepMzRange ( ) const

get mz range that results in max setQscore

◆ getScanNumber()

int getScanNumber ( ) const

get scan number

◆ getSNR()

float getSNR ( ) const

get total SNR

◆ getTargetDecoyType()

PeakGroup::TargetDecoyType getTargetDecoyType ( ) const

get the target decoy type of this

◆ isPositive()

bool isPositive ( ) const

get if it is positive mode

◆ isSignalMZ()

bool isSignalMZ	(	double	mz,
		double	tol
	)		const

determine is an mz is a signal of this peakgroup. Input tol is ppm tolerance (e.g., 10.0 for 10ppm tolerance). Assume logMzPeaks are sorted.

◆ isTargeted()

bool isTargeted ( ) const

get if it is targeted

◆ operator<()

bool operator< ( const PeakGroup & a ) const

comparison operators

◆ operator=()

PeakGroup& operator= ( const PeakGroup & t )

default

assignment operator

◆ operator==()

bool operator== ( const PeakGroup & a ) const

◆ operator>()

bool operator> ( const PeakGroup & a ) const

◆ operator[]()

const FLASHDeconvHelperStructs::LogMzPeak& operator[] ( Size i ) const

◆ push_back()

void push_back ( const FLASHDeconvHelperStructs::LogMzPeak & pg )

vector operators for the LogMzPeaks in this PeakGroup

◆ recruitAllPeaksInSpectrum()

std::vector<LogMzPeak> recruitAllPeaksInSpectrum	(	const MSSpectrum &	spec,
		double	tol,
		const FLASHDeconvHelperStructs::PrecalculatedAveragine &	avg,
		double	mono_mass
	)

given a monoisotopic mass, recruit raw peaks from the raw input spectrum and add to this peakGroup. This is a bit time-consuming and is done for only a small number of selected high-quality peakgroups.

Parameters

spec	raw spectrum
tol	ppm tolerance
avg	precalculated averagine
mono_mass	monoisotopic mass

Returns: returns the noisy peaks for this peakgroup - i.e., the raw peaks within the range of this peakGroup that are not matched to any istope of this peakGroup mass.

◆ reserve()

void reserve ( Size n )

◆ setAbsChargeRange()

void setAbsChargeRange	(	int	min_abs_charge,
		int	max_abs_charge
	)

set min_abs_charge and max_abs_charge charge range

◆ setAvgPPMError()

void setAvgPPMError ( float error )

set average mass ppm error

◆ setChargeIsotopeCosine()

void setChargeIsotopeCosine	(	int	abs_charge,
		float	cos
	)

set per abs_charge isotope cosine

◆ setChargeScore()

void setChargeScore ( float charge_score )

set charge score - for FLASHIda log file parsing

◆ setChargeSNR()

void setChargeSNR	(	int	abs_charge,
		float	c_snr
	)

set charge SNR manually - for FLASHIda log file parsing

◆ setFeatureIndex()

void setFeatureIndex ( uint findex )

set feature index

◆ setIndex()

void setIndex ( uint i )

set index of this peak group

◆ setIsotopeCosine()

void setIsotopeCosine ( float cos )

set isotope cosine score

◆ setIsotopeDaDistance()

void setIsotopeDaDistance ( double d )

set distance between consecutive isotopes

◆ setMonoisotopicMass()

void setMonoisotopicMass ( double mono_mass )

set monoisotopic mass

◆ setQscore()

void setQscore ( double qscore )

set Q score - for FLASHIda log file parsing

◆ setQscore2D()

void setQscore2D ( double fqscore )

set Q score 2D

◆ setQvalue()

void setQvalue	(	double	q,
		PeakGroup::TargetDecoyType	target_decoy_type
	)

set peakGroup q value for different TargetDecoyType. Q values are stored per TargetDecoyType and later used for final q value calculation.

Parameters

target_decoy_type This target_decoy_type specifies if a PeakGroup is a target (0), charge decoy (1), noise decoy (2), or isotope decoy (3)

◆ setRepAbsCharge()

void setRepAbsCharge ( int max_snr_abs_charge )

set representative max_snr_abs_charge

◆ setScanNumber()

void setScanNumber ( int scan_number )

set scan number

◆ setSNR()

void setSNR ( float snr )

set SNR manually - for FLASHIda log file parsing

◆ setTargetDecoyType()

void setTargetDecoyType ( PeakGroup::TargetDecoyType index )

for this PeakGroup, specify the target decoy type.

◆ setTargeted()

void setTargeted ( )

set if it is targeted

◆ size()

Size size ( ) const

noexcept

◆ sort()

void sort ( )

◆ swap()

void swap ( std::vector< FLASHDeconvHelperStructs::LogMzPeak > & x )

◆ updateAvgDaError_()

void updateAvgDaError_ ( )

private

update avg Da error

◆ updateAvgPPMError_()

void updateAvgPPMError_ ( )

private

update avg ppm error

◆ updateChargeFitScoreAndChargeIntensities_()

void updateChargeFitScoreAndChargeIntensities_ ( bool is_low_charge )

private

update chargefit score and also update per charge intensities here.

◆ updateChargeRange_()

void updateChargeRange_ ( std::vector< LogMzPeak > & noisy_peaks )

private

update the charge range using the calculated per charge information

◆ updateMonoMassAndIsotopeIntensities()

void updateMonoMassAndIsotopeIntensities ( )

add monoisotopic indices of peaks by offset and discard negative isotope peaks. Total intensity is also updated

◆ updatePerChargeCos_()

void updatePerChargeCos_ ( const FLASHDeconvHelperStructs::PrecalculatedAveragine & avg )

private

update per charge cosine values

◆ updatePerChargeInformation_()

void updatePerChargeInformation_ ( const std::vector< LogMzPeak > & noisy_peaks )

private

update per charge intensities, noise power, and squared intensities. used for SNR estimation

◆ updateQscore()

int updateQscore	(	std::vector< LogMzPeak > &	noisy_peaks,
		const FLASHDeconvHelperStructs::PrecalculatedAveragine &	avg,
		double	min_cos,
		bool	is_low_charge,
		bool	is_profile = `false`,
		int	allowed_iso_error = `1`
	)

Update setQscore. Cosine and SNRs are also updated.

Parameters

noisy_peaks	noisy peaks to calculate setQscore
avg	precalculated averagine
min_cos	the peak groups with cosine score less than this will have setQscore 0.
is_low_charge	if set, charge fit score calculation becomes less harshy
is_profile	if input spectrum is a profile spectrum or now
allowed_iso_error	this set the allowed isotope error in decoy mass generation.

Returns: returns isotope offset after isotope cosine calculation

◆ updateSNR_()

void updateSNR_ ( )

private

using signal and total (signal + noise) power, update SNR value

Member Data Documentation

◆ avg_da_error_

float avg_da_error_ = 0

private

◆ avg_ppm_error_

float avg_ppm_error_ = 0

private

◆ bin_width_DL_

float bin_width_DL_ = 0.25

private

◆ charge_range_for_DL_

int charge_range_for_DL_ = 7

private

◆ charge_score_

float charge_score_ = 0

private

◆ dl_matrices_

std::vector<Matrix<float> > dl_matrices_

private

◆ findex_

uint findex_ = 0

private

feature index

◆ index_

uint index_ = 0

private

peak group index

◆ intensity_

float intensity_ = 0

private

◆ is_positive_

bool is_positive_ = false

private

is positive or not

◆ is_targeted_

bool is_targeted_ = false

private

if this peak group has been targeted

◆ iso_da_distance_

double iso_da_distance_ = Constants::ISOTOPE_MASSDIFF_55K_U

private

distance between consecutive isotopes. Can be different for decoys

◆ iso_range_for_DL_

int iso_range_for_DL_ = 21

private

◆ isotope_cosine_score_

float isotope_cosine_score_ = 0

private

◆ logMzpeaks_

std::vector<FLASHDeconvHelperStructs::LogMzPeak> logMzpeaks_

private

log Mz peaks

◆ max_abs_charge_

int max_abs_charge_ = -1

private

◆ max_snr_abs_charge_

int max_snr_abs_charge_ = -1

private

scoring variables

◆ min_abs_charge_

int min_abs_charge_ = 0

private

charge range

◆ min_negative_isotope_index_

int min_negative_isotope_index_ = -1

private

up to which negative isotope index should be considered. By considereing negative istoopes, one can reduce isotope index error.

◆ monoisotopic_mass_

double monoisotopic_mass_ = -1.0

private

information on the deconvolved mass

◆ negative_iso_peaks_

std::vector<FLASHDeconvHelperStructs::LogMzPeak> negative_iso_peaks_

private

negative isotope index peaks

◆ per_charge_cos_

std::vector<float> per_charge_cos_

private

◆ per_charge_int_

std::vector<float> per_charge_int_

private

◆ per_charge_noise_pwr_

std::vector<float> per_charge_noise_pwr_

private

◆ per_charge_snr_

std::vector<float> per_charge_snr_

private

◆ per_charge_sum_signal_squared_

std::vector<float> per_charge_sum_signal_squared_

private

per charge SNR, isotope cosine, and intensity vectors

◆ per_isotope_int_

std::vector<float> per_isotope_int_

private

per isotope intensity.

◆ qscore2D_

double qscore2D_ = -1.0f

private

◆ qscore_

double qscore_ = .0f

private

◆ qvalue_

std::map<PeakGroup::TargetDecoyType, float> qvalue_

private

q values with different decoy types

◆ scan_number_

int scan_number_ = 0

private

scan number

◆ snr_

float snr_ = 0

private

◆ target_decoy_type_

PeakGroup::TargetDecoyType target_decoy_type_ = target

private

index to specify if this peak_group is a target (0), an isotope decoy (1), a noise (2), or a charge decoy (3)

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ LogMzPeak

◆ PrecalculatedAveragine

Member Enumeration Documentation

◆ TargetDecoyType

Constructor & Destructor Documentation

◆ PeakGroup() [1/4]

◆ PeakGroup() [2/4]

◆ ~PeakGroup()

◆ PeakGroup() [3/4]

◆ PeakGroup() [4/4]

Member Function Documentation

◆ back()

◆ begin() [1/2]

◆ begin() [2/2]

◆ calculateDLMatrices()

◆ clear_()

◆ empty()

◆ end() [1/2]

◆ end() [2/2]

◆ getAbsChargeRange()

◆ getAbsDaError_()

◆ getAbsPPMError_()

◆ getAvgDaError()

◆ getAvgPPMError()

◆ getBinWidthDL()

◆ getChargeIntensity()

◆ getChargeIsotopeCosine()

◆ getChargeRangeForDL()

◆ getChargeScore()

◆ getChargeSNR()

◆ getDLMatrix()

◆ getFeatureIndex()

◆ getIndex()

◆ getIntensity()

◆ getIsotopeCosine()

◆ getIsotopeDaDistance()

◆ getIsotopeIntensities()

◆ getIsotopeRangeForDL()

◆ getMinNegativeIsotopeIndex()

◆ getMonoMass()

◆ getMzRange()

◆ getNoisePeakBegin() [1/2]

◆ getNoisePeakBegin() [2/2]

◆ getNoisePeakEnd() [1/2]

◆ getNoisePeakEnd() [2/2]

◆ getNoisePeakPower_()

◆ getQscore()

◆ getQscore2D()

◆ getQvalue()

◆ getRepAbsCharge()

◆ getRepMzRange()

◆ getScanNumber()

◆ getSNR()

◆ getTargetDecoyType()

◆ isPositive()

◆ isSignalMZ()

◆ isTargeted()

◆ operator<()

◆ operator=()

◆ operator==()

◆ operator>()

◆ operator[]()

◆ push_back()

◆ recruitAllPeaksInSpectrum()

◆ reserve()

◆ setAbsChargeRange()

◆ setAvgPPMError()

◆ setChargeIsotopeCosine()

◆ setChargeScore()

◆ setChargeSNR()

◆ setFeatureIndex()

◆ setIndex()

◆ setIsotopeCosine()