FLASHIda class for real time deconvolution This class contains functions to perform deconvolution (by SpectralDeconvolution) 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 FLASHHelperClasses::PrecalculatedAveragine	PrecalculatedAveragine

typedef FLASHHelperClasses::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, int length, double rt, int ms_level, const char name, const char cv)
	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, int ids)
	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...

void	removeFromExlusionList (int id)
	Remove a given precursor from the exclusion list by id (needed for FAIMS) More...

double	getRepresentativeMass ()

void	getAllMonoisotopicMasses (double *masses, int length)

int	GetAllPeakGroupSize ()

Static Public Member Functions
static std::map< int, std::vector< std::vector< float > > >	parseFLASHIdaLog (const String &in_log_file)
	parse FLASHIda log file More...

Private Member Functions
void	filterPeakGroupsUsingMassExclusion_ (int ms_level, double rt)
	discard peak groups using mass exclusion More...

Static Private Member Functions
static MSSpectrum	makeMSSpectrum_ (const double mzs, const double ints, int length, double rt, 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
std::unordered_map< int, double >	tqscore_exceeding_mz_rt_map_
	PeakGroup comparator for soring by QScore. 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...

std::unordered_map< int, int >	id_mass_map_
	mass value vs. total qscore for all acquired precursors More...

std::unordered_map< int, int >	id_mz_map_

std::unordered_map< int, double >	id_qscore_map_

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

DeconvolvedSpectrum	selected_peak_groups_
	selected peak groups out of deconvolved_spectrum_ 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_

std::vector< int >	trigger_ids_

SpectralDeconvolution	fd_
	SpectralDeconvolution class for deconvolution. More...

double	tqscore_threshold = .99
	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...

int	targeting_mode_ = 0

std::map< double, std::vector< double > >	target_mass_rt_map_
	0 no targeting 1 inclusive 2 exclusive More...

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

std::vector< double >	target_masses_

int	window_id_ = 0
	current target masses. updated per spectrum More...

std::map< double, std::vector< double > >	exclusion_rt_masses_map_
	maps for global exclusion More...

std::vector< double >	excluded_masses_
	if rt == 0, its mapped masses are always excluded. More...

double	snr_threshold_ = 1
	current target masses. updated per spectrum More...

DoubleList	tol_
	mass tolerance More...

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

Detailed Description

FLASHIda class for real time deconvolution This class contains functions to perform deconvolution (by SpectralDeconvolution) 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: FLASHIdaBridgeFunction, https://stackoverflow.com/questions/31417688/passing-a-vector-array-from-unmanaged-c-to-c-sharp

Member Typedef Documentation

◆ LogMzPeak

typedef FLASHHelperClasses::LogMzPeak LogMzPeak

◆ PrecalculatedAveragine

typedef FLASHHelperClasses::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_	(	int	ms_level,
		double	rt
	)

private

discard peak groups using mass exclusion

Parameters

ms_level	MS level
rt	Retention time

◆ getAllMonoisotopicMasses()

void getAllMonoisotopicMasses	(	double *	masses,
		int	length
	)

◆ GetAllPeakGroupSize()

int GetAllPeakGroupSize ( )

◆ 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,
		int *	ids
	)

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
ids	precursor IDs

◆ getPeakGroups()

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

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
cv	CV values when FAIMS is used

Returns: number of acquired peak groups

◆ getRepresentativeMass()

double getRepresentativeMass ( )

◆ makeMSSpectrum_()

static MSSpectrum makeMSSpectrum_	(	const double *	mzs,
		const double *	ints,
		int	length,
		double	rt,
		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

◆ parseFLASHIdaLog()

static std::map<int, std::vector<std::vector<float> > > parseFLASHIdaLog ( const String & in_log_file )

static

parse FLASHIda log file

Parameters

in_log_file input log file

Returns: parsed information : scan number - percursor information

◆ removeFromExlusionList()

void removeFromExlusionList ( int id )

Remove a given precursor from the exclusion list by id (needed for FAIMS)

Parameters

id	id of precursor

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

◆ cv_to_mass_

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

private

Initial value:

= {
      {-80.0, {2400.0, 2900.0}},
      {-70.0, {3500.0, 4000.0}},
      {-60.0, {4500.0, 5000.0}},
      {-50.0, {5100.0, 6500.0}},
      {-40.0, {7500.0, 10000.0}},
      {-30.0, {11000.0, 14000.0}},
      {-20.0, {12000.0, 15000.0}},
      {-10.0, {13000.0, 15500.0}},
      {-0.0, {14000.0, 16000.0}},
      {10.0, {15000.0, 16500.0}},
    }

◆ deconvolved_spectrum_

DeconvolvedSpectrum deconvolved_spectrum_

private

deconvolved spectrum that contains the peak group

◆ excluded_masses_

std::vector<double> excluded_masses_

private

if rt == 0, its mapped masses are always excluded.

◆ exclusion_rt_masses_map_

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

private

maps for global exclusion

◆ fd_

SpectralDeconvolution fd_

private

SpectralDeconvolution class for deconvolution.

◆ id_mass_map_

std::unordered_map<int, int> id_mass_map_

private

mass value vs. total qscore for all acquired precursors

Maps that are neccessary for selectively disabling mass exclusion (needed for FAIMS support)

◆ id_mz_map_

std::unordered_map<int, int> id_mz_map_

private

◆ id_qscore_map_

std::unordered_map<int, double> id_qscore_map_

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

◆ qscore_threshold_

double qscore_threshold_

private

q score threshold - determined from C# side

◆ rt_window_

double rt_window_

private

retention time window - determined from C# side

◆ selected_peak_groups_

DeconvolvedSpectrum selected_peak_groups_

private

selected peak groups out of deconvolved_spectrum_

◆ snr_threshold_

double snr_threshold_ = 1

private

current target masses. updated per spectrum

precursor SNR threshold

◆ target_mass_qscore_map_

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

private

◆ target_mass_rt_map_

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

private

0 no targeting 1 inclusive 2 exclusive

maps for global inclusion targeting

◆ target_masses_

std::vector<double> target_masses_

private

◆ targeting_mode_

int targeting_mode_ = 0

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

PeakGroup comparator for soring by QScore.

Maps that are necessary for mass exclusion

◆ tqscore_threshold

double tqscore_threshold = .99

private

total QScore threshold

◆ trigger_charges

std::vector<int> trigger_charges

private

peakGroup charges to be triggered

◆ trigger_ids_

std::vector<int> trigger_ids_

private

◆ 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

◆ window_id_

int window_id_ = 0

private

current target masses. updated per spectrum

Public Types

Public Member Functions

Static 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_()

◆ getAllMonoisotopicMasses()

◆ GetAllPeakGroupSize()

◆ getIsolationWindows()

◆ getPeakGroups()

◆ getRepresentativeMass()

◆ makeMSSpectrum_()

◆ operator=()

◆ parseFLASHIdaLog()

◆ removeFromExlusionList()

Member Data Documentation

◆ all_mass_rt_map_

◆ cv_to_mass_

◆ deconvolved_spectrum_

◆ excluded_masses_

◆ exclusion_rt_masses_map_

◆ fd_

◆ id_mass_map_

◆ id_mz_map_

◆ id_qscore_map_

◆ mass_count_

◆ mass_qscore_map_

◆ qscore_threshold_

◆ rt_window_

◆ selected_peak_groups_

◆ snr_threshold_

◆ target_mass_qscore_map_

◆ target_mass_rt_map_

◆ target_masses_

◆ targeting_mode_

◆ tol_

◆ tqscore_exceeding_mass_rt_map_

◆ tqscore_exceeding_mz_rt_map_

◆ tqscore_threshold

◆ trigger_charges

◆ trigger_ids_

◆ trigger_left_isolation_mzs_

◆ trigger_right_isolation_mzs_

◆ window_id_