Quality Control function for OpenSwath. More...

#include <OpenMS/ANALYSIS/OPENSWATH/SwathQC.h>

Collaboration diagram for SwathQC:

Public Types
typedef std::map< int, int >	ChargeDistribution

Public Member Functions
	SwathQC ()=delete
	default C'tor (forbidden) More...

	SwathQC (const size_t cd_spectra, const double decon_ms1_mz_tol)
	CTor with arguments. More...

std::function< void(const OpenMS::ExperimentalSettings &es)>	getExpSettingsFunc ()
	Returns a lambda function, which captures internal members and can be used in MSDataTransformingConsumer::setExperimentalSettingsFunc() More...

std::function< void(const OpenMS::MSSpectrum &)>	getSpectraProcessingFunc ()

void	storeJSON (const OpenMS::String &filename)
	Save all internally collected data to a JSON file. More...

const ChargeDistribution &	getChargeDistribution () const
	returns the charge distribution which was internally computed by applying getSpectraProcessingFunc() externally More...

void	setNrMS1Spectra (size_t nr)
	Explicitly set the number of expected MS1 spectra (for sampling charge distribution) More...

Static Public Member Functions
static ChargeDistribution	getChargeDistribution (const std::vector< SwathMap > &swath_maps, const size_t nr_samples, const double mz_tol)
	Sample the spectra in all MS1 Swath maps and determine all charge states. More...

Static Protected Member Functions
static bool	isSubsampledSpectrum_ (const size_t total_spec_count, const size_t subsample_count, const size_t idx)
	Given a total spectrum count and a number of spectra to inspect, is the current index a candidate? More...

Private Attributes
ChargeDistribution	cd_
	internal ChargeDistribution which is augmented upon calling the corresponding member functions More...

size_t	nr_ms1_spectra_
	number of MS1 spectra expected More...

size_t	cd_spectra_
	number of spectra to inspect for charge distribution More...

double	decon_ms1_mz_tol_
	m/z tolerance for isotope deconvolution More...

size_t	ms1_spectra_seen_
	keeps track of number of spectra passed to getSpectraProcessingFunc() More...

Detailed Description

Quality Control function for OpenSwath.

The class is meant to collect information as a plugin of type IMSDataConsumer. You can (if the relevant data is already available and you do not mind the overhead), call static functions, which will do the same.

Member Typedef Documentation

◆ ChargeDistribution

typedef std::map<int,int> ChargeDistribution

Constructor & Destructor Documentation

◆ SwathQC() [1/2]

SwathQC ( )

delete

default C'tor (forbidden)

◆ SwathQC() [2/2]

SwathQC	(	const size_t	cd_spectra,
		const double	decon_ms1_mz_tol
	)

CTor with arguments.

Parameters

cd_spectra	Number of MS spectra to inspect for charge distribution estimation
decon_ms1_mz_tol	m/z tolerance for isotope deconvolution

Member Function Documentation

◆ getChargeDistribution() [1/2]

const ChargeDistribution& getChargeDistribution ( ) const

returns the charge distribution which was internally computed by applying getSpectraProcessingFunc() externally

◆ getChargeDistribution() [2/2]

static ChargeDistribution getChargeDistribution	(	const std::vector< SwathMap > &	swath_maps,
		const size_t	nr_samples,
		const double	mz_tol
	)

static

Sample the spectra in all MS1 Swath maps and determine all charge states.

Conveniently wraps internal functions and applies them to a whole set of data. However, it might be more speed efficient to sample the spectra as they are loaded using member functions.

From all swath maps in swath_maps which are ms_level == 1 we extract nr_samples spectra (subsampling), determine the charge states of all isotopic envelopes and return their total counts using getSpectraProcessingFunc().

Parameters

[in]	swath_maps	Swath maps of mixed ms-level
[in]	nr_samples	Number of spectra to sample per Swath map. To sample all spectra, set to -1
[in]	mz_tol	Error tolerance in Th in which an isotopic peak is expected (assuming C12-C13 distance)

Returns: Distribution of charge (key = charge, value = counts)

Exceptions

Exception::Postcondition if Deisotoper did not return charge data

◆ getExpSettingsFunc()

std::function<void(const OpenMS::ExperimentalSettings& es)> getExpSettingsFunc ( )

Returns a lambda function, which captures internal members and can be used in MSDataTransformingConsumer::setExperimentalSettingsFunc()

If es contains a metavalue 'nr_ms1_spectra' it will be used to set the internal number of expected MS1 spectra

◆ getSpectraProcessingFunc()

std::function<void (const OpenMS::MSSpectrum&)> getSpectraProcessingFunc ( )

returns a lambda function, which captures internal members and can be used in MSDataTransformingConsumer::setExperimentalSettingsFunc() PeakPicking is performed internally if the data is estimated to be profile data. Uses the Deisotoper class for charge determination and updates the internal charge count.

◆ isSubsampledSpectrum_()

static bool isSubsampledSpectrum_	(	const size_t	total_spec_count,
		const size_t	subsample_count,
		const size_t	idx
	)

staticprotected

Given a total spectrum count and a number of spectra to inspect, is the current index a candidate?

Allows to uniformly sample a range of spectra. E.g. given 10 spectra exist, and we want to subsample 4 of them, the answer of this function for every requested index from 0..9 is:

If the total number of spectra is unknown, pass 0 as first argument, which will return true for every query, i.e. sample everything.

Parameters

[in]	total_spec_count	Total number of spectra expected
[in]	subsample_count	Number of spectra which should be sampled from `total_spec_count`
[in]	idx	Index of the spectrum under question

◆ setNrMS1Spectra()

void setNrMS1Spectra ( size_t nr )

Explicitly set the number of expected MS1 spectra (for sampling charge distribution)

Computing the charge distribution using getSpectraProcessingFunc() requires knowing the total number of MS1 spectra. Either use getExpSettingsFunc() externally, or use this method to set it explicitly (depending on workflow). If nr is set to 0, all spectra passed into getSpectraProcessingFunc() will be inspected for their charge distribution.

◆ storeJSON()

void storeJSON ( const OpenMS::String & filename )

Save all internally collected data to a JSON file.

Member Data Documentation

◆ cd_

ChargeDistribution cd_

private

internal ChargeDistribution which is augmented upon calling the corresponding member functions

◆ cd_spectra_

size_t cd_spectra_

private

number of spectra to inspect for charge distribution

◆ decon_ms1_mz_tol_

double decon_ms1_mz_tol_

private

m/z tolerance for isotope deconvolution

◆ ms1_spectra_seen_

size_t ms1_spectra_seen_

private

keeps track of number of spectra passed to getSpectraProcessingFunc()

◆ nr_ms1_spectra_

size_t nr_ms1_spectra_

private

number of MS1 spectra expected

Public Types

Public Member Functions

Static Public Member Functions

Static Protected Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ ChargeDistribution

Constructor & Destructor Documentation

◆ SwathQC() [1/2]

◆ SwathQC() [2/2]

Member Function Documentation

◆ getChargeDistribution() [1/2]

◆ getChargeDistribution() [2/2]

◆ getExpSettingsFunc()

◆ getSpectraProcessingFunc()

◆ isSubsampledSpectrum_()

◆ setNrMS1Spectra()

◆ storeJSON()

Member Data Documentation

◆ cd_

◆ cd_spectra_

◆ decon_ms1_mz_tol_

◆ ms1_spectra_seen_

◆ nr_ms1_spectra_