FLASHIda class for real time deconvolution This class contains functions to perform deconvolution (by FLASHDeconvAlgorithm) for the spectrum received from Thermo iAPI. Also precursor selection is done in this class. The functions in this class are invoked in C# Thermo iAPI side through the functions in FLASHIdaBridgeFunctions class. More...

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

Collaboration diagram for FLASHIda:

[legend]

Public Types
typedef FLASHDeconvHelperStructs::PrecalculatedAveragine	PrecalculatedAveragine

typedef FLASHDeconvHelperStructs::LogMzPeak	LogMzPeak

Public Member Functions
	FLASHIda (char *arg)
	constructor that takes string input argument More...

	~FLASHIda ()=default
	destructor More...

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

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

FLASHIda &	operator= (const FLASHIda &fd)=default
	assignment operator More...

int	getPeakGroups (const double mzs, const double intensities, const int length, const double rt, const int ms_level, const char *name)
	get peak groups (deconvolved masses) from input spectrum, specified by mzs and intensities (due to C# interface it is necessary) More...

void	getIsolationWindows (double window_start, double window_end, double qscores, int charges, int min_charges, int max_charges, double mono_masses, double charge_cos, double charge_snrs, double iso_cos, double snrs, double charge_scores, double ppm_errors, double precursor_intensities, double *peakgroup_intensities)
	get isolation windows using FLASHDeconv algorithm. Many parameters are in primitive types so they can be passed to C# FLASHIda side. All parameters are for isolation windows. More...

Private Member Functions
void	filterPeakGroupsUsingMassExclusion_ (const int ms_level, const double rt)
	mass value vs. retention time for all acquired precursors More...

Static Private Member Functions
static MSSpectrum	makeMSSpectrum_ (const double mzs, const double ints, const int length, const double rt, const int ms_level, const char *name)
	generate MSSpectrum class using mzs and intensities. mzs and intensities and other information are provided by Thermo iAPI More...

Private Attributes
struct {
}	QscoreComparator_
	PeakGroup comparator for soring by QScore. More...

std::unordered_map< int, double >	tqscore_exceeding_mz_rt_map_
	Maps that are necessary for mass exclusion. More...

std::unordered_map< int, double >	tqscore_exceeding_mass_rt_map_
	integer mz value vs. retention time with tqscore exceeding total qscore threshold More...

std::unordered_map< int, double >	all_mass_rt_map_
	integer mass value vs. retention time with tqscore exceeding total qscore threshold More...

std::unordered_map< int, double >	mass_qscore_map_
	mz value vs. retention time for all acquired precursors More...

DeconvolvedSpectrum	deconvolved_spectrum_
	deconvolved spectrum that contains the peak group More...

std::vector< int >	trigger_charges
	peakGroup charges to be triggered More...

std::vector< double >	trigger_left_isolation_mzs_
	peakGroup isolation window ranges More...

std::vector< double >	trigger_right_isolation_mzs_

FLASHDeconvAlgorithm	fd_
	FLASHDeconvAlgorithm class for deconvolution. More...

double	tqscore_threshold = .9
	total QScore threshold More...

double	qscore_threshold_
	q score threshold - determined from C# side More...

double	rt_window_
	retention time window - determined from C# side More...

IntList	mass_count_
	how many masses will be selected per ms level? - determined from C# side More...

const double	min_isolation_window_half_ = .6
	minimum isolation window width divided by two More...

const double	max_isolation_window_half_ = 3.0
	maximum isolation window width divided by two More...

bool	inclusive_mode_ = true

std::map< double, std::vector< double > >	target_mass_rt_map_
	maps for global inclusion targeting More...

std::map< double, std::vector< double > >	target_mz_rt_map_

std::vector< double >	target_masses_

std::map< double, std::vector< double > >	excluded_mass_rt_map_
	current target masses More...

std::map< double, std::vector< double > >	excluded_mz_rt_map_

std::vector< double >	excluded_masses_

double	snr_threshold_ = 1.0
	current target masses More...

DoubleList	tol_
	mass tolerance More...

Detailed Description

FLASHIda class for real time deconvolution This class contains functions to perform deconvolution (by FLASHDeconvAlgorithm) for the spectrum received from Thermo iAPI. Also precursor selection is done in this class. The functions in this class are invoked in C# Thermo iAPI side through the functions in FLASHIdaBridgeFunctions class.

See also: FLASHIdaBridgeFunctions @reference: https://stackoverflow.com/questions/31417688/passing-a-vector-array-from-unmanaged-c-to-c-sharp

Member Typedef Documentation

◆ LogMzPeak

typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak

◆ PrecalculatedAveragine

typedef FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine

Constructor & Destructor Documentation

◆ FLASHIda() [1/3]

FLASHIda ( char * arg )

explicit

constructor that takes string input argument

◆ ~FLASHIda()

~FLASHIda ( )

default

destructor

◆ FLASHIda() [2/3]

FLASHIda ( const FLASHIda & )

default

copy constructor

◆ FLASHIda() [3/3]

FLASHIda ( FLASHIda && other )

default

move constructor

Member Function Documentation

◆ filterPeakGroupsUsingMassExclusion_()

void filterPeakGroupsUsingMassExclusion_	(	const int	ms_level,
		const double	rt
	)

private

mass value vs. retention time for all acquired precursors

discard peak groups using mass exclusion

Parameters

ms_level	MS level
rt	Retention time

◆ getIsolationWindows()

void getIsolationWindows	(	double *	window_start,
		double *	window_end,
		double *	qscores,
		int *	charges,
		int *	min_charges,
		int *	max_charges,
		double *	mono_masses,
		double *	charge_cos,
		double *	charge_snrs,
		double *	iso_cos,
		double *	snrs,
		double *	charge_scores,
		double *	ppm_errors,
		double *	precursor_intensities,
		double *	peakgroup_intensities
	)

get isolation windows using FLASHDeconv algorithm. Many parameters are in primitive types so they can be passed to C# FLASHIda side. All parameters are for isolation windows.

Parameters

window_start	window start mzs
window_end	window end mzs
qscores	QScores of windows
charges	charges of windows
min_charges	minimum charges
max_charges	maximum charges
mono_masses	monoisotopic masses
charge_cos	charge cosine scores
charge_snrs	charge SNRs or precursor SNRs
iso_cos	mass cosine scores
snrs	mass SNRs
charge_scores	charge distribution scores
ppm_errors	average PPM errors
precursor_intensities	precursor peak intensities
peakgroup_intensities	precursor mass intensities

◆ getPeakGroups()

int getPeakGroups	(	const double *	mzs,
		const double *	intensities,
		const int	length,
		const double	rt,
		const int	ms_level,
		const char *	name
	)

get peak groups (deconvolved masses) from input spectrum, specified by mzs and intensities (due to C# interface it is necessary)

Parameters

mzs	mz values of the input spectrum
intensities	intensities of the input spectrum
length	length of mzs and ints
rt	Retention time in seconds
ms_level	ms level
name	spectrum name

Returns: number of peak groups

◆ makeMSSpectrum_()

static MSSpectrum makeMSSpectrum_	(	const double *	mzs,
		const double *	ints,
		const int	length,
		const double	rt,
		const int	ms_level,
		const char *	name
	)

staticprivate

generate MSSpectrum class using mzs and intensities. mzs and intensities and other information are provided by Thermo iAPI

Parameters

mzs	m/z values
ints	intensities
length	number of peaks
rt	Retention time
ms_level	MS level
name	spectrum name

◆ operator=()

FLASHIda& operator= ( const FLASHIda & fd )

default

assignment operator

Member Data Documentation

◆ all_mass_rt_map_

std::unordered_map<int, double> all_mass_rt_map_

private

integer mass value vs. retention time with tqscore exceeding total qscore threshold

◆ deconvolved_spectrum_

DeconvolvedSpectrum deconvolved_spectrum_

private

deconvolved spectrum that contains the peak group

◆ excluded_mass_rt_map_

std::map<double, std::vector<double> > excluded_mass_rt_map_

private

current target masses

maps for global exclusion targeting

◆ excluded_masses_

std::vector<double> excluded_masses_

private

◆ excluded_mz_rt_map_

std::map<double, std::vector<double> > excluded_mz_rt_map_

private

◆ fd_

FLASHDeconvAlgorithm fd_

private

FLASHDeconvAlgorithm class for deconvolution.

◆ inclusive_mode_

bool inclusive_mode_ = true

private

◆ mass_count_

IntList mass_count_

private

how many masses will be selected per ms level? - determined from C# side

◆ mass_qscore_map_

std::unordered_map<int, double> mass_qscore_map_

private

mz value vs. retention time for all acquired precursors

◆ max_isolation_window_half_

const double max_isolation_window_half_ = 3.0

private

maximum isolation window width divided by two

◆ min_isolation_window_half_

const double min_isolation_window_half_ = .6

private

minimum isolation window width divided by two

◆ qscore_threshold_

double qscore_threshold_

private

q score threshold - determined from C# side

◆

struct { ... } QscoreComparator_

PeakGroup comparator for soring by QScore.

◆ rt_window_

double rt_window_

private

retention time window - determined from C# side

◆ snr_threshold_

double snr_threshold_ = 1.0

private

current target masses

precursor SNR threshold

◆ target_mass_rt_map_

std::map<double, std::vector<double> > target_mass_rt_map_

private

maps for global inclusion targeting

◆ target_masses_

std::vector<double> target_masses_

private

◆ target_mz_rt_map_

std::map<double, std::vector<double> > target_mz_rt_map_

private

◆ tol_

DoubleList tol_

private

mass tolerance

◆ tqscore_exceeding_mass_rt_map_

std::unordered_map<int, double> tqscore_exceeding_mass_rt_map_

private

integer mz value vs. retention time with tqscore exceeding total qscore threshold

◆ tqscore_exceeding_mz_rt_map_

std::unordered_map<int, double> tqscore_exceeding_mz_rt_map_

private

Maps that are necessary for mass exclusion.

◆ tqscore_threshold

double tqscore_threshold = .9

private

total QScore threshold

◆ trigger_charges

std::vector<int> trigger_charges

private

peakGroup charges to be triggered

◆ trigger_left_isolation_mzs_

std::vector<double> trigger_left_isolation_mzs_

private

peakGroup isolation window ranges

◆ trigger_right_isolation_mzs_

std::vector<double> trigger_right_isolation_mzs_

private

Public Types

Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ LogMzPeak

◆ PrecalculatedAveragine

Constructor & Destructor Documentation

◆ FLASHIda() [1/3]

◆ ~FLASHIda()

◆ FLASHIda() [2/3]

◆ FLASHIda() [3/3]

Member Function Documentation

◆ filterPeakGroupsUsingMassExclusion_()

◆ getIsolationWindows()

◆ getPeakGroups()

◆ makeMSSpectrum_()

◆ operator=()

Member Data Documentation

◆ all_mass_rt_map_

◆ deconvolved_spectrum_

◆ excluded_mass_rt_map_

◆ excluded_masses_

◆ excluded_mz_rt_map_

◆ fd_

◆ inclusive_mode_

◆ mass_count_

◆ mass_qscore_map_

◆ max_isolation_window_half_

◆ min_isolation_window_half_

◆ qscore_threshold_

◆

◆ rt_window_

◆ snr_threshold_

◆ target_mass_rt_map_

◆ target_masses_

◆ target_mz_rt_map_

◆ tol_

◆ tqscore_exceeding_mass_rt_map_

◆ tqscore_exceeding_mz_rt_map_

◆ tqscore_threshold

◆ trigger_charges

◆ trigger_left_isolation_mzs_

◆ trigger_right_isolation_mzs_