Implements different algorithms for precursor ion selection. More...

#include <OpenMS/ANALYSIS/TARGETED/OfflinePrecursorIonSelection.h>

Inheritance diagram for OfflinePrecursorIonSelection:

Collaboration diagram for OfflinePrecursorIonSelection:

Classes
struct	PairComparatorSecondElement

Public Types
typedef PSLPFormulation::IndexTriple	IndexTriple

Public Member Functions
	OfflinePrecursorIonSelection ()

	~OfflinePrecursorIonSelection () override

void	makePrecursorSelectionForKnownLCMSMap (const FeatureMap &features, const PeakMap &experiment, PeakMap &ms2, std::set< Int > &charges_set, bool feature_based)
	Makes the precursor selection for a given feature map, either feature or scan based. More...

void	getMassRanges (const FeatureMap &features, const PeakMap &experiment, std::vector< std::vector< std::pair< Size, Size > > > &indices)
	Calculates the mass ranges for each feature and stores them as indices of the raw data. More...

void	createProteinSequenceBasedLPInclusionList (String include, String rt_model_file, String pt_model_file, FeatureMap &precursors)

void	setLPSolver (LPWrapper::SOLVER solver)

LPWrapper::SOLVER	getLPSolver ()

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Private Types
typedef std::map< std::pair< double, double >, int, PairComparatorSecondElement< std::pair< double, double > > >	ExclusionListType_

Private Member Functions
void	calculateXICs_ (const FeatureMap &features, const std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const PeakMap &experiment, const std::set< Int > &charges_set, std::vector< std::vector< std::pair< Size, double > > > &xics)
	Calculate the sum of intensities of relevant features for each scan separately. More...

void	checkMassRanges_ (std::vector< std::vector< std::pair< Size, Size > > > &mass_ranges, const PeakMap &experiment)
	Eliminates overlapping peaks. More...

void	updateExclusionList_ (ExclusionListType_ &exclusion_list) const
	reduce scan count for each entry, and remove every entry which has reached 0 counts More...

Private Attributes
LPWrapper::SOLVER	solver_

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

Implements different algorithms for precursor ion selection.

Implements different algorithms for precursor ion selection, either based on a whole FeatureMap (e.g. like with LC-MALDI MS data) or based on single scans (e.g. with LC-ESI MS data).

Member Typedef Documentation

◆ ExclusionListType_

typedef std::map<std::pair<double, double>, int, PairComparatorSecondElement<std::pair<double, double> > > ExclusionListType_

private

◆ IndexTriple

typedef PSLPFormulation::IndexTriple IndexTriple

Constructor & Destructor Documentation

◆ OfflinePrecursorIonSelection()

OfflinePrecursorIonSelection ( )

◆ ~OfflinePrecursorIonSelection()

~OfflinePrecursorIonSelection ( )

override

Member Function Documentation

◆ calculateXICs_()

void calculateXICs_	(	const FeatureMap &	features,
		const std::vector< std::vector< std::pair< Size, Size > > > &	mass_ranges,
		const PeakMap &	experiment,
		const std::set< Int > &	charges_set,
		std::vector< std::vector< std::pair< Size, double > > > &	xics
	)

private

Calculate the sum of intensities of relevant features for each scan separately.

◆ checkMassRanges_()

void checkMassRanges_	(	std::vector< std::vector< std::pair< Size, Size > > > &	mass_ranges,
		const PeakMap &	experiment
	)

private

Eliminates overlapping peaks.

◆ createProteinSequenceBasedLPInclusionList()

void createProteinSequenceBasedLPInclusionList	(	String	include,
		String	rt_model_file,
		String	pt_model_file,
		FeatureMap &	precursors
	)

◆ getLPSolver()

LPWrapper::SOLVER getLPSolver ( )

inline

◆ getMassRanges()

void getMassRanges	(	const FeatureMap &	features,
		const PeakMap &	experiment,
		std::vector< std::vector< std::pair< Size, Size > > > &	indices
	)

Calculates the mass ranges for each feature and stores them as indices of the raw data.

Parameters

features	Input feature map
experiment	Input raw data
indices	The boundaries of the features as indices in the raw data

◆ makePrecursorSelectionForKnownLCMSMap()

void makePrecursorSelectionForKnownLCMSMap	(	const FeatureMap &	features,
		const PeakMap &	experiment,
		PeakMap &	ms2,
		std::set< Int > &	charges_set,
		bool	feature_based
	)

Makes the precursor selection for a given feature map, either feature or scan based.

Parameters

features	Input feature map
experiment	Input raw data
ms2	Precursors are added as empty MS2 spectra to this MSExperiment
charges_set	Allowed charge states
feature_based	If true the selection is feature based, if false it is scan based and the highest signals in each spectrum are chosen

◆ setLPSolver()

void setLPSolver ( LPWrapper::SOLVER solver )

inline

◆ updateExclusionList_()

void updateExclusionList_ ( ExclusionListType_ & exclusion_list ) const

private

reduce scan count for each entry, and remove every entry which has reached 0 counts

Member Data Documentation

◆ solver_

LPWrapper::SOLVER solver_

private

Classes

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ExclusionListType_

◆ IndexTriple

Constructor & Destructor Documentation

◆ OfflinePrecursorIonSelection()

◆ ~OfflinePrecursorIonSelection()

Member Function Documentation

◆ calculateXICs_()

◆ checkMassRanges_()

◆ createProteinSequenceBasedLPInclusionList()

◆ getLPSolver()

◆ getMassRanges()

◆ makePrecursorSelectionForKnownLCMSMap()

◆ setLPSolver()

◆ updateExclusionList_()

Member Data Documentation

◆ solver_