#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmMetaboIdent.h>

Inheritance diagram for FeatureFinderAlgorithmMetaboIdent:

Collaboration diagram for FeatureFinderAlgorithmMetaboIdent:

Classes
struct	FeatureCompare
	Comparison functor for features. More...

struct	FeatureFilterQuality
	Predicate for filtering features by overall quality. More...

struct	FeatureFinderMetaboIdentCompound
	represents a compound in the assay library More...

struct	MassTraceBounds
	Boundaries for a mass trace in a feature. More...

Public Member Functions
	FeatureFinderAlgorithmMetaboIdent ()
	default constructor More...

void	run (const std::vector< FeatureFinderMetaboIdentCompound > &metaboIdentTable, FeatureMap &features, String spectra_file="")
	perform targeted feature extraction of compounds from More...

PeakMap &	getMSData ()
	Retrieve chromatograms (empty if run was not executed) More...

const PeakMap &	getMSData () const

void	setMSData (const PeakMap &m)
	Set spectra. More...

void	setMSData (PeakMap &&m)

const PeakMap &	getChromatograms () const
	Retrieve chromatograms (empty if run was not executed) More...

PeakMap &	getChromatograms ()

const TargetedExperiment &	getLibrary () const
	Retrieve the assay library (e.g., to store as TraML, empty if run was not executed) More...

const TransformationDescription &	getTransformations () const
	Retrieve deviations between provided coordinates and extracted ones (e.g., to store as TrafoXML or for plotting) More...

size_t	getNShared () const
	Retrieve number of features with shared identifications. More...

String	prettyPrintCompound (const TargetedExperiment::Compound &compound)

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...

virtual 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...

Protected Types
typedef std::map< UInt64, std::vector< MassTraceBounds > >	FeatureBoundsMap
	Boundaries for all mass traces per feature. More...

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace	MassTrace

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces	MassTraces

typedef std::vector< Feature * >	FeatureGroup
	group of (overlapping) features More...

Protected Member Functions
void	extractTransformations_ (const FeatureMap &features)

void	addTargetToLibrary_ (const String &name, const String &formula, double mass, const std::vector< Int > &charges, const std::vector< double > &rts, std::vector< double > rt_ranges, const std::vector< double > &iso_distrib)
	Add a target (from the input file) to the assay library. More...

Size	addTargetAnnotations_ (FeatureMap &features)
	Add "peptide" identifications with information about targets to features. More...

void	addTargetRT_ (TargetedExperiment::Compound &target, double rt)

double	calculateMZ_ (double mass, Int charge) const
	Calculate mass-to-charge ratio from mass and charge. More...

void	generateTransitions_ (const String &target_id, double mz, Int charge, const IsotopeDistribution &iso_dist)

bool	hasOverlappingBounds_ (const std::vector< MassTraceBounds > &mtb1, const std::vector< MassTraceBounds > &mtb2) const
	Check if two sets of mass trace boundaries overlap. More...

void	getFeatureBounds_ (const FeatureMap &features, FeatureBoundsMap &feature_bounds)

bool	hasOverlappingFeature_ (const Feature &feature, const FeatureGroup &group, const FeatureBoundsMap &feature_bounds) const

void	findOverlappingFeatures_ (FeatureMap &features, const FeatureBoundsMap &feature_bounds, std::vector< FeatureGroup > &overlap_groups)

void	resolveOverlappingFeatures_ (FeatureGroup &group, const FeatureBoundsMap &feature_bounds)

void	annotateFeatures_ (FeatureMap &features)

void	ensureConvexHulls_ (Feature &feature) const

void	selectFeaturesFromCandidates_ (FeatureMap &features)

void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
struct OpenMS::FeatureFinderAlgorithmMetaboIdent::FeatureFilterQuality	feature_filter_

struct OpenMS::FeatureFinderAlgorithmMetaboIdent::FeatureCompare	feature_compare_

double	rt_window_
	RT window width. More...

double	mz_window_
	m/z window width More...

bool	mz_window_ppm_
	m/z window width is given in PPM (not Da)? More...

double	isotope_pmin_
	min. isotope probability for peptide assay More...

Size	n_isotopes_
	number of isotopes for peptide assay More...

double	peak_width_

double	min_peak_width_

double	signal_to_noise_

String	elution_model_

String	candidates_out_

Size	debug_level_

PeakMap	ms_data_
	input LC-MS data More...

PeakMap	chrom_data_
	accumulated chromatograms (XICs) More...

MRMFeatureFinderScoring	feat_finder_
	OpenSWATH feature finder. More...

TargetedExperiment	library_
	accumulated assays for targets More...

TransformationDescription	trafo_

CoarseIsotopePatternGenerator	iso_gen_
	isotope pattern generator More...

std::map< String, double >	isotope_probs_
	isotope probabilities of transitions More...

std::map< String, double >	target_rts_
	RTs of targets (assays) More...

size_t	n_shared_ = 0

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...

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...

Class Documentation

◆ OpenMS::FeatureFinderAlgorithmMetaboIdent::MassTraceBounds

struct OpenMS::FeatureFinderAlgorithmMetaboIdent::MassTraceBounds

Boundaries for a mass trace in a feature.

Collaboration diagram for FeatureFinderAlgorithmMetaboIdent::MassTraceBounds:

[legend]

Class Members
double	mz_max
double	mz_min
double	rt_max
double	rt_min
Size	sub_index

Member Typedef Documentation

◆ FeatureBoundsMap

typedef std::map<UInt64, std::vector<MassTraceBounds> > FeatureBoundsMap

protected

Boundaries for all mass traces per feature.

◆ FeatureGroup

typedef std::vector<Feature*> FeatureGroup

protected

group of (overlapping) features

◆ MassTrace

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace

protected

◆ MassTraces

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces

protected

Constructor & Destructor Documentation

◆ FeatureFinderAlgorithmMetaboIdent()

FeatureFinderAlgorithmMetaboIdent ( )

default constructor

Member Function Documentation

◆ addTargetAnnotations_()

Size addTargetAnnotations_ ( FeatureMap & features )

protected

Add "peptide" identifications with information about targets to features.

◆ addTargetRT_()

void addTargetRT_	(	TargetedExperiment::Compound &	target,
		double	rt
	)

protected

◆ addTargetToLibrary_()

void addTargetToLibrary_	(	const String &	name,
		const String &	formula,
		double	mass,
		const std::vector< Int > &	charges,
		const std::vector< double > &	rts,
		std::vector< double >	rt_ranges,
		const std::vector< double > &	iso_distrib
	)

protected

Add a target (from the input file) to the assay library.

◆ annotateFeatures_()

void annotateFeatures_ ( FeatureMap & features )

protected

◆ calculateMZ_()

double calculateMZ_	(	double	mass,
		Int	charge
	)		const

protected

Calculate mass-to-charge ratio from mass and charge.

◆ ensureConvexHulls_()

void ensureConvexHulls_ ( Feature & feature ) const

protected

◆ extractTransformations_()

void extractTransformations_ ( const FeatureMap & features )

protected

◆ findOverlappingFeatures_()

void findOverlappingFeatures_	(	FeatureMap &	features,
		const FeatureBoundsMap &	feature_bounds,
		std::vector< FeatureGroup > &	overlap_groups
	)

protected

◆ generateTransitions_()

void generateTransitions_	(	const String &	target_id,
		double	mz,
		Int	charge,
		const IsotopeDistribution &	iso_dist
	)

protected

◆ getChromatograms() [1/2]

PeakMap& getChromatograms ( )

inline

◆ getChromatograms() [2/2]

const PeakMap& getChromatograms ( ) const

inline

Retrieve chromatograms (empty if run was not executed)

◆ getFeatureBounds_()

void getFeatureBounds_	(	const FeatureMap &	features,
		FeatureBoundsMap &	feature_bounds
	)

protected

◆ getLibrary()

const TargetedExperiment& getLibrary ( ) const

inline

Retrieve the assay library (e.g., to store as TraML, empty if run was not executed)

◆ getMSData() [1/2]

PeakMap& getMSData ( )

inline

Retrieve chromatograms (empty if run was not executed)

◆ getMSData() [2/2]

const PeakMap& getMSData ( ) const

inline

◆ getNShared()

size_t getNShared ( ) const

inline

Retrieve number of features with shared identifications.

◆ getTransformations()

const TransformationDescription& getTransformations ( ) const

inline

Retrieve deviations between provided coordinates and extracted ones (e.g., to store as TrafoXML or for plotting)

◆ hasOverlappingBounds_()

bool hasOverlappingBounds_	(	const std::vector< MassTraceBounds > &	mtb1,
		const std::vector< MassTraceBounds > &	mtb2
	)		const

protected

Check if two sets of mass trace boundaries overlap.

◆ hasOverlappingFeature_()

bool hasOverlappingFeature_	(	const Feature &	feature,
		const FeatureGroup &	group,
		const FeatureBoundsMap &	feature_bounds
	)		const

protected

◆ prettyPrintCompound()

String prettyPrintCompound ( const TargetedExperiment::Compound & compound )

◆ resolveOverlappingFeatures_()

void resolveOverlappingFeatures_	(	FeatureGroup &	group,
		const FeatureBoundsMap &	feature_bounds
	)

protected

◆ run()

void run	(	const std::vector< FeatureFinderMetaboIdentCompound > &	metaboIdentTable,
		FeatureMap &	features,
		String	spectra_file = `""`
	)

perform targeted feature extraction of compounds from

Parameters

metaboIdentTable	and stores them in
feature.	If `spectra_file` is provided it will be used as a fall-back to setPrimaryMSRunPath in the feature map in case a proper primaryMSRunPath is not annotated in the MSExperiment.

◆ selectFeaturesFromCandidates_()

void selectFeaturesFromCandidates_ ( FeatureMap & features )

protected

◆ setMSData() [1/2]

void setMSData ( const PeakMap & m )

Set spectra.

◆ setMSData() [2/2]

void setMSData ( PeakMap && m )

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ candidates_out_

String candidates_out_

protected

◆ chrom_data_

PeakMap chrom_data_

protected

accumulated chromatograms (XICs)

◆ debug_level_

Size debug_level_

protected

◆ elution_model_

String elution_model_

protected

◆ feat_finder_

MRMFeatureFinderScoring feat_finder_

protected

OpenSWATH feature finder.

◆ feature_compare_

struct OpenMS::FeatureFinderAlgorithmMetaboIdent::FeatureCompare feature_compare_

protected

◆ feature_filter_

struct OpenMS::FeatureFinderAlgorithmMetaboIdent::FeatureFilterQuality feature_filter_

protected

◆ iso_gen_

CoarseIsotopePatternGenerator iso_gen_

protected

isotope pattern generator

◆ isotope_pmin_

double isotope_pmin_

protected

min. isotope probability for peptide assay

◆ isotope_probs_

std::map<String, double> isotope_probs_

protected

isotope probabilities of transitions

◆ library_

TargetedExperiment library_

protected

accumulated assays for targets

◆ min_peak_width_

double min_peak_width_

protected

◆ ms_data_

PeakMap ms_data_

protected

input LC-MS data

◆ mz_window_

double mz_window_

protected

m/z window width

◆ mz_window_ppm_

bool mz_window_ppm_

protected

m/z window width is given in PPM (not Da)?

◆ n_isotopes_

Size n_isotopes_

protected

number of isotopes for peptide assay

◆ n_shared_

size_t n_shared_ = 0

protected

◆ peak_width_

double peak_width_

protected

◆ rt_window_

double rt_window_

protected

RT window width.

◆ signal_to_noise_

double signal_to_noise_

protected

◆ target_rts_

std::map<String, double> target_rts_

protected

RTs of targets (assays)

◆ trafo_

TransformationDescription trafo_

protected

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Class Documentation

◆ OpenMS::FeatureFinderAlgorithmMetaboIdent::MassTraceBounds

Member Typedef Documentation

◆ FeatureBoundsMap

◆ FeatureGroup

◆ MassTrace

◆ MassTraces

Constructor & Destructor Documentation

◆ FeatureFinderAlgorithmMetaboIdent()

Member Function Documentation

◆ addTargetAnnotations_()

◆ addTargetRT_()

◆ addTargetToLibrary_()

◆ annotateFeatures_()

◆ calculateMZ_()

◆ ensureConvexHulls_()

◆ extractTransformations_()

◆ findOverlappingFeatures_()

◆ generateTransitions_()

◆ getChromatograms() [1/2]

◆ getChromatograms() [2/2]

◆ getFeatureBounds_()

◆ getLibrary()

◆ getMSData() [1/2]

◆ getMSData() [2/2]

◆ getNShared()

◆ getTransformations()

◆ hasOverlappingBounds_()

◆ hasOverlappingFeature_()

◆ prettyPrintCompound()

◆ resolveOverlappingFeatures_()

◆ run()

◆ selectFeaturesFromCandidates_()

◆ setMSData() [1/2]

◆ setMSData() [2/2]

◆ updateMembers_()

Member Data Documentation

◆ candidates_out_

◆ chrom_data_

◆ debug_level_

◆ elution_model_

◆ feat_finder_

◆ feature_compare_

◆ feature_filter_

◆ iso_gen_

◆ isotope_pmin_

◆ isotope_probs_

◆ library_

◆ min_peak_width_

◆ ms_data_

◆ mz_window_

◆ mz_window_ppm_

◆ n_isotopes_

◆ n_shared_

◆ peak_width_

◆ rt_window_

◆ signal_to_noise_

◆ target_rts_

◆ trafo_