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

Inheritance diagram for FeatureFinderIdentificationAlgorithm:

Collaboration diagram for FeatureFinderIdentificationAlgorithm:

Classes
struct	FeatureCompare
	comparison functor for features More...

struct	FeatureFilterPeptides
	predicate for filtering features by assigned peptides: More...

struct	FeatureFilterQuality
	predicate for filtering features by overall quality: More...

struct	PeptideCompare
	comparison functor for (unassigned) peptide IDs More...

struct	RTRegion
	region in RT in which a peptide elutes: More...

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

void	run (std::vector< PeptideIdentification > peptides, const std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > peptides_ext, std::vector< ProteinIdentification > proteins_ext, FeatureMap &features, const FeatureMap &seeds=FeatureMap(), const String &spectra_file="")

void	runOnCandidates (FeatureMap &features)

PeakMap &	getMSData ()

const PeakMap &	getMSData () const

void	setMSData (const PeakMap &ms_data)
	set the MS data used for feature detection More...

void	setMSData (PeakMap &&ms_data)

PeakMap &	getChromatograms ()

const PeakMap &	getChromatograms () const

ProgressLogger &	getProgressLogger ()

const ProgressLogger &	getProgressLogger () const

TargetedExperiment &	getLibrary ()

const TargetedExperiment &	getLibrary () const

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...

Protected Types
typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace	MassTrace

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces	MassTraces

typedef std::multimap< double, PeptideIdentification * >	RTMap
	mapping: RT (not necessarily unique) -> pointer to peptide More...

typedef std::map< Int, std::pair< RTMap, RTMap > >	ChargeMap
	mapping: charge -> internal/external: (RT -> pointer to peptide) More...

typedef std::map< AASequence, ChargeMap >	PeptideMap
	mapping: sequence -> charge -> internal/external ID information More...

typedef std::map< String, std::pair< RTMap, RTMap > >	PeptideRefRTMap
	mapping: peptide ref. -> int./ext.: (RT -> pointer to peptide) More...

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

void	generateTransitions_ (const String &peptide_id, double mz, Int charge, const IsotopeDistribution &iso_dist)
	generate transitions (isotopic traces) for a peptide ion and add them to the library: More...

void	addPeptideRT_ (TargetedExperiment::Peptide &peptide, double rt) const

void	getRTRegions_ (ChargeMap &peptide_data, std::vector< RTRegion > &rt_regions, bool clear_IDs=true) const
	get regions in which peptide eludes (ideally only one) by clustering RT elution times More...

void	annotateFeaturesFinalizeAssay_ (FeatureMap &features, std::map< Size, std::vector< PeptideIdentification * > > &feat_ids, RTMap &rt_internal)

void	annotateFeatures_ (FeatureMap &features, PeptideRefRTMap &ref_rt_map)
	annotate identified features with m/z, isotope probabilities, etc. More...

void	ensureConvexHulls_ (Feature &feature) const

void	postProcess_ (FeatureMap &features, bool with_external_ids)

void	statistics_ (const FeatureMap &features) const
	some statistics on detected features More...

void	createAssayLibrary_ (const PeptideMap::iterator &begin, const PeptideMap::iterator &end, PeptideRefRTMap &ref_rt_map, bool clear_IDs=true)

void	addPeptideToMap_ (PeptideIdentification &peptide, PeptideMap &peptide_map, bool external=false)

void	checkNumObservations_ (Size n_pos, Size n_neg, const String &note="") const

void	getUnbiasedSample_ (const std::multimap< double, std::pair< Size, bool > > &valid_obs, std::map< Size, double > &training_labels)

void	getRandomSample_ (std::map< Size, double > &training_labels) const

void	classifyFeatures_ (FeatureMap &features)

void	filterFeaturesFinalizeAssay_ (Feature &best_feature, double best_quality, const double quality_cutoff)

void	filterFeatures_ (FeatureMap &features, bool classified)

void	calculateFDR_ (FeatureMap &features)

Size	addSeeds_ (std::vector< PeptideIdentification > &peptides, const FeatureMap &seeds)

Size	addOffsetPeptides_ (std::vector< PeptideIdentification > &peptides, double offset)

template<typename It >
std::vector< std::pair< It, It > >	chunk_ (It range_from, It range_to, const std::ptrdiff_t batch_size)

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

Protected Attributes
PeptideMap	peptide_map_

Size	n_internal_peps_
	number of internal peptide More...

Size	n_external_peps_
	number of external peptides More...

Size	batch_size_
	nr of peptides to use at the same time during chromatogram extraction More...

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	mapping_tolerance_
	RT tolerance for mapping IDs to features. More...

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

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

double	rt_quantile_

double	peak_width_

double	min_peak_width_

double	signal_to_noise_

String	elution_model_

double	svm_min_prob_

StringList	svm_predictor_names_

String	svm_xval_out_

double	svm_quality_cutoff

Size	svm_n_parts_
	number of partitions for SVM cross-validation More...

Size	svm_n_samples_
	number of samples for SVM training More...

String	candidates_out_

Size	debug_level_

struct OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterQuality	feature_filter_quality_

struct OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides	feature_filter_peptides_

struct OpenMS::FeatureFinderIdentificationAlgorithm::PeptideCompare	peptide_compare_

struct OpenMS::FeatureFinderIdentificationAlgorithm::FeatureCompare	feature_compare_

PeakMap	ms_data_
	input LC-MS data More...

PeakMap	chrom_data_
	accumulated chromatograms (XICs) More...

TargetedExperiment	library_
	accumulated assays for peptides More...

bool	quantify_decoys_

double	add_mass_offset_peptides_ {0.0}
	non-zero if for every feature an additional offset features should be extracted More...

bool	use_psm_cutoff_

double	psm_score_cutoff_

std::vector< PeptideIdentification >	unassignedIDs_

const double	seed_rt_window_ = 60.0
	extraction window used for seeds (smaller than rt_window_ as we know the exact apex positions) More...

std::map< double, std::pair< Size, Size > >	svm_probs_internal_
	SVM probability -> number of pos./neg. features (for FDR calculation): More...

std::multiset< double >	svm_probs_external_
	SVM probabilities for "external" features (for FDR calculation): More...

Size	n_internal_features_
	internal feature counter (for FDR calculation) More...

Size	n_external_features_

TransformationDescription	trafo_external_
	TransformationDescription trafo_; // RT transformation (to range 0-1) More...

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

MRMFeatureFinderScoring	feat_finder_
	OpenSWATH feature finder. More...

ProgressLogger	prog_log_

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::FeatureFinderIdentificationAlgorithm::RTRegion

struct OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion

region in RT in which a peptide elutes:

Collaboration diagram for FeatureFinderIdentificationAlgorithm::RTRegion:

[legend]

Class Members
double	end
ChargeMap	ids	internal/external peptide IDs (per charge) in this region
double	start

Member Typedef Documentation

◆ ChargeMap

typedef std::map<Int, std::pair<RTMap, RTMap> > ChargeMap

protected

mapping: charge -> internal/external: (RT -> pointer to peptide)

◆ MassTrace

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace

protected

◆ MassTraces

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces

protected

◆ PeptideMap

typedef std::map<AASequence, ChargeMap> PeptideMap

protected

mapping: sequence -> charge -> internal/external ID information

◆ PeptideRefRTMap

typedef std::map<String, std::pair<RTMap, RTMap> > PeptideRefRTMap

protected

mapping: peptide ref. -> int./ext.: (RT -> pointer to peptide)

◆ RTMap

typedef std::multimap<double, PeptideIdentification*> RTMap

protected

mapping: RT (not necessarily unique) -> pointer to peptide

Constructor & Destructor Documentation

◆ FeatureFinderIdentificationAlgorithm()

FeatureFinderIdentificationAlgorithm ( )

default constructor

Member Function Documentation

◆ addOffsetPeptides_()

Size addOffsetPeptides_	(	std::vector< PeptideIdentification > &	peptides,
		double	offset
	)

protected

◆ addPeptideRT_()

void addPeptideRT_	(	TargetedExperiment::Peptide &	peptide,
		double	rt
	)		const

protected

◆ addPeptideToMap_()

void addPeptideToMap_	(	PeptideIdentification &	peptide,
		PeptideMap &	peptide_map,
		bool	external = `false`
	)

protected

CAUTION: This method stores a pointer to the given peptide reference in internals Make sure it stays valid until destruction of the class.

Todo:: find better solution

◆ addSeeds_()

Size addSeeds_	(	std::vector< PeptideIdentification > &	peptides,
		const FeatureMap &	seeds
	)

protected

◆ annotateFeatures_()

void annotateFeatures_	(	FeatureMap &	features,
		PeptideRefRTMap &	ref_rt_map
	)

protected

annotate identified features with m/z, isotope probabilities, etc.

◆ annotateFeaturesFinalizeAssay_()

void annotateFeaturesFinalizeAssay_	(	FeatureMap &	features,
		std::map< Size, std::vector< PeptideIdentification * > > &	feat_ids,
		RTMap &	rt_internal
	)

protected

◆ calculateFDR_()

void calculateFDR_ ( FeatureMap & features )

protected

◆ checkNumObservations_()

void checkNumObservations_	(	Size	n_pos,
		Size	n_neg,
		const String &	note = `""`
	)		const

protected

◆ chunk_()

std::vector<std::pair<It,It> > chunk_	(	It	range_from,
		It	range_to,
		const std::ptrdiff_t	batch_size
	)

inlineprotected

Chunks an iterator range (allowing advance and distance) into batches of size batch_size. Last batch might be smaller.

◆ classifyFeatures_()

void classifyFeatures_ ( FeatureMap & features )

protected

◆ createAssayLibrary_()

void createAssayLibrary_	(	const PeptideMap::iterator &	begin,
		const PeptideMap::iterator &	end,
		PeptideRefRTMap &	ref_rt_map,
		bool	clear_IDs = `true`
	)

protected

creates an assay library out of the peptide sequences and their RT elution windows the PeptideMap is mutable since we clear it on-the-go

Parameters

clear_IDs set to false to keep IDs in internal charge maps (only needed for debugging purposes)

◆ ensureConvexHulls_()

void ensureConvexHulls_ ( Feature & feature ) const

protected

◆ filterFeatures_()

void filterFeatures_	(	FeatureMap &	features,
		bool	classified
	)

protected

◆ filterFeaturesFinalizeAssay_()

void filterFeaturesFinalizeAssay_	(	Feature &	best_feature,
		double	best_quality,
		const double	quality_cutoff
	)

protected

◆ generateTransitions_()

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

protected

generate transitions (isotopic traces) for a peptide ion and add them to the library:

◆ getChromatograms() [1/2]

PeakMap& getChromatograms ( )

◆ getChromatograms() [2/2]

const PeakMap& getChromatograms ( ) const

◆ getLibrary() [1/2]

TargetedExperiment& getLibrary ( )

◆ getLibrary() [2/2]

const TargetedExperiment& getLibrary ( ) const

◆ getMSData() [1/2]

PeakMap& getMSData ( )

◆ getMSData() [2/2]

const PeakMap& getMSData ( ) const

◆ getProgressLogger() [1/2]

ProgressLogger& getProgressLogger ( )

◆ getProgressLogger() [2/2]

const ProgressLogger& getProgressLogger ( ) const

◆ getRandomSample_()

void getRandomSample_ ( std::map< Size, double > & training_labels ) const

protected

◆ getRTRegions_()

void getRTRegions_	(	ChargeMap &	peptide_data,
		std::vector< RTRegion > &	rt_regions,
		bool	clear_IDs = `true`
	)		const

protected

get regions in which peptide eludes (ideally only one) by clustering RT elution times

◆ getUnbiasedSample_()

void getUnbiasedSample_	(	const std::multimap< double, std::pair< Size, bool > > &	valid_obs,
		std::map< Size, double > &	training_labels
	)

protected

◆ postProcess_()

void postProcess_	(	FeatureMap &	features,
		bool	with_external_ids
	)

protected

◆ run()

void run	(	std::vector< PeptideIdentification >	peptides,
		const std::vector< ProteinIdentification > &	proteins,
		std::vector< PeptideIdentification >	peptides_ext,
		std::vector< ProteinIdentification >	proteins_ext,
		FeatureMap &	features,
		const FeatureMap &	seeds = `FeatureMap()`,
		const String &	spectra_file = `""`
	)

Main method for actual FeatureFinder External IDs (peptides_ext, proteins_ext) may be empty, in which case no machine learning or FDR estimation will be performed. Optional seeds from e.g. untargeted FeatureFinders can be added with seeds. Results will be written to features. Note: The primaryMSRunPath of features will be updated to the primaryMSRunPath stored in the MSExperiment. If that path is not a valid and readable mzML spectra_file will be annotated as a fall-back. Caution: peptide IDs will be shrunk to best hit, FFid metavalues added and potential seed IDs added.

◆ runOnCandidates()

void runOnCandidates ( FeatureMap & features )

◆ setMSData() [1/2]

void setMSData ( const PeakMap & ms_data )

set the MS data used for feature detection

◆ setMSData() [2/2]

void setMSData ( PeakMap && ms_data )

◆ statistics_()

void statistics_ ( const FeatureMap & features ) const

protected

some statistics on detected features

◆ 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

◆ add_mass_offset_peptides_

double add_mass_offset_peptides_ {0.0}

protected

non-zero if for every feature an additional offset features should be extracted

◆ batch_size_

Size batch_size_

protected

nr of peptides to use at the same time during chromatogram extraction

◆ 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::FeatureFinderIdentificationAlgorithm::FeatureCompare feature_compare_

protected

◆ feature_filter_peptides_

struct OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides feature_filter_peptides_

protected

◆ feature_filter_quality_

struct OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterQuality feature_filter_quality_

protected

◆ 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 peptides

◆ mapping_tolerance_

double mapping_tolerance_

protected

RT tolerance for mapping IDs to features.

◆ 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_external_features_

Size n_external_features_

protected

external feature counter (for FDR calculation)

◆ n_external_peps_

Size n_external_peps_

protected

number of external peptides

◆ n_internal_features_

Size n_internal_features_

protected

internal feature counter (for FDR calculation)

◆ n_internal_peps_

Size n_internal_peps_

protected

number of internal peptide

◆ n_isotopes_

Size n_isotopes_

protected

number of isotopes for peptide assay

◆ peak_width_

double peak_width_

protected

◆ peptide_compare_

struct OpenMS::FeatureFinderIdentificationAlgorithm::PeptideCompare peptide_compare_

protected

◆ peptide_map_

PeptideMap peptide_map_

protected

◆ prog_log_

ProgressLogger prog_log_

protected

◆ psm_score_cutoff_

double psm_score_cutoff_

protected

◆ quantify_decoys_

bool quantify_decoys_

protected

◆ rt_quantile_

double rt_quantile_

protected

◆ rt_window_

double rt_window_

protected

RT window width.

◆ seed_rt_window_

const double seed_rt_window_ = 60.0

protected

extraction window used for seeds (smaller than rt_window_ as we know the exact apex positions)

◆ signal_to_noise_

double signal_to_noise_

protected

◆ svm_min_prob_

double svm_min_prob_

protected

◆ svm_n_parts_

Size svm_n_parts_

protected

number of partitions for SVM cross-validation

◆ svm_n_samples_

Size svm_n_samples_

protected

number of samples for SVM training

◆ svm_predictor_names_

StringList svm_predictor_names_

protected

◆ svm_probs_external_

std::multiset<double> svm_probs_external_

protected

SVM probabilities for "external" features (for FDR calculation):

◆ svm_probs_internal_

std::map<double, std::pair<Size, Size> > svm_probs_internal_

protected

SVM probability -> number of pos./neg. features (for FDR calculation):

◆ svm_quality_cutoff

double svm_quality_cutoff

protected

◆ svm_xval_out_

String svm_xval_out_

protected

◆ trafo_external_

TransformationDescription trafo_external_

protected

TransformationDescription trafo_; // RT transformation (to range 0-1)

transform. to external RT scale

◆ unassignedIDs_

std::vector<PeptideIdentification> unassignedIDs_

protected

◆ use_psm_cutoff_

bool use_psm_cutoff_

protected

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Class Documentation

◆ OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion

Member Typedef Documentation

◆ ChargeMap

◆ MassTrace

◆ MassTraces

◆ PeptideMap

◆ PeptideRefRTMap

◆ RTMap

Constructor & Destructor Documentation

◆ FeatureFinderIdentificationAlgorithm()

Member Function Documentation

◆ addOffsetPeptides_()

◆ addPeptideRT_()

◆ addPeptideToMap_()

◆ addSeeds_()

◆ annotateFeatures_()

◆ annotateFeaturesFinalizeAssay_()

◆ calculateFDR_()

◆ checkNumObservations_()

◆ chunk_()

◆ classifyFeatures_()

◆ createAssayLibrary_()

◆ ensureConvexHulls_()

◆ filterFeatures_()

◆ filterFeaturesFinalizeAssay_()

◆ generateTransitions_()

◆ getChromatograms() [1/2]

◆ getChromatograms() [2/2]

◆ getLibrary() [1/2]

◆ getLibrary() [2/2]

◆ getMSData() [1/2]

◆ getMSData() [2/2]

◆ getProgressLogger() [1/2]

◆ getProgressLogger() [2/2]

◆ getRandomSample_()

◆ getRTRegions_()

◆ getUnbiasedSample_()

◆ postProcess_()

◆ run()

◆ runOnCandidates()

◆ setMSData() [1/2]

◆ setMSData() [2/2]

◆ statistics_()

◆ updateMembers_()

Member Data Documentation

◆ add_mass_offset_peptides_

◆ batch_size_

◆ candidates_out_

◆ chrom_data_

◆ debug_level_

◆ elution_model_

◆ feat_finder_

◆ feature_compare_

◆ feature_filter_peptides_

◆ feature_filter_quality_

◆ isotope_pmin_

◆ isotope_probs_

◆ library_

◆ mapping_tolerance_

◆ min_peak_width_

◆ ms_data_

◆ mz_window_

◆ mz_window_ppm_

◆ n_external_features_

◆ n_external_peps_

◆ n_internal_features_

◆ n_internal_peps_

◆ n_isotopes_

◆ peak_width_

◆ peptide_compare_

◆ peptide_map_

◆ prog_log_

◆ psm_score_cutoff_