Class for handling external peptide identifications in feature finding. More...

#include <OpenMS/FEATUREFINDER/FFIDAlgoExternalIDHandler.h>

Collaboration diagram for FFIDAlgoExternalIDHandler:

Public Types
typedef std::multimap< double, PeptideIdentification * >	ExternalRTMap
	RTMap for external data structure storage. More...

typedef std::map< Int, ExternalRTMap >	ExternalChargeMap
	Charge to External RTMap mapping. More...

typedef std::map< AASequence, ExternalChargeMap >	ExternalPeptideMap
	Sequence to External Charge Map mapping. More...

Public Member Functions
	FFIDAlgoExternalIDHandler ()
	Default constructor. More...

void	reset ()
	Reset the handler's state. More...

void	addExternalPeptide (PeptideIdentification &peptide)
	Add an external peptide to the handler's map. More...

void	processExternalPeptides (std::vector< PeptideIdentification > &peptides_ext)
	Process external peptide IDs. More...

double	alignInternalAndExternalIDs (const std::vector< PeptideIdentification > &peptides_internal, const std::vector< PeptideIdentification > &peptides_external, double rt_quantile)
	Align internal and external IDs to estimate RT shifts and return RT uncertainty. More...

double	transformRT (double rt) const
	Transform RT from internal to external scale. More...

bool	hasRTTransformation () const
	Check if we have RT transformation data. More...

const TransformationDescription &	getRTTransformation () const
	Get the RT transformation. More...

void	classifyFeaturesWithSVM (FeatureMap &features, const Param &param)
	Classify features using SVM. More...

void	filterClassifiedFeatures (FeatureMap &features, double quality_cutoff)
	Filter classified features. More...

void	calculateFDR (FeatureMap &features)
	Calculate FDR for classified features. More...

const std::map< double, std::pair< Size, Size > > &	getSVMProbsInternal () const
	Get SVM probabilities for internal features. More...

Private Member Functions
void	addExternalPeptideToMap_ (PeptideIdentification &peptide, std::map< AASequence, std::map< Int, std::pair< std::multimap< double, PeptideIdentification * >, std::multimap< double, PeptideIdentification * >>>> &peptide_map)
	Add external peptide to charge map (merged version for compatibility) More...

bool	fillExternalRTMap_ (const AASequence &sequence, Int charge, std::multimap< double, PeptideIdentification * > &rt_map)
	Fill an external RTMap from our data for a specific peptide and charge. More...

void	annotateFeatureWithExternalIDs_ (Feature &feature)
	Check and set feature class based on external data. More...

void	initSVMParameters_ (const Param &param)
	Initialize SVM parameters. More...

void	finalizeAssayFeatures_ (Feature &best_feature, double best_quality, double quality_cutoff)
	Finalize assay features. More...

void	getRandomSample_ (std::map< Size, double > &training_labels)
	Get random sample for SVM training. More...

void	checkNumObservations_ (Size n_pos, Size n_neg, const String &note="") const
	Check observation counts for SVM. More...

void	getUnbiasedSample_ (const std::multimap< double, std::pair< Size, bool > > &valid_obs, std::map< Size, double > &training_labels)
	Get unbiased sample for SVM training. More...

void	addDummyPeptideID_ (Feature &feature, const PeptideIdentification *ext_id)
	Add dummy peptide identification from external data. More...

void	handleExternalFeature_ (Feature &feature, double prob_positive, double quality_cutoff)
	Handle external feature probability. More...

void	adjustFDRForExternalFeatures_ (std::vector< double > &fdr_probs, std::vector< double > &fdr_qvalues, Size n_internal_features)
	Adjust FDR calculation for external features. More...

Private Attributes
ExternalPeptideMap	external_peptide_map_
	External peptide storage. More...

TransformationDescription	rt_transformation_
	RT transformation description. More...

Size	n_external_peptides_
	Number of external peptides. More...

Size	n_external_features_
	Number of external features. More...

std::multiset< double >	svm_probs_external_
	SVM probabilities for external features. More...

std::map< double, std::pair< Size, Size > >	svm_probs_internal_
	SVM probabilities for internal features. More...

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

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

double	svm_min_prob_
	SVM minimum probability threshold. More...

double	svm_quality_cutoff
	SVM quality cutoff. More...

std::vector< String >	svm_predictor_names_
	SVM predictor names. More...

String	svm_xval_out_
	SVM cross-validation output file. More...

Int	debug_level_
	Debug level. More...

Size	n_internal_features_
	Number of internal features. More...

Detailed Description

Class for handling external peptide identifications in feature finding.

This class encapsulates all functionality related to external peptide IDs in the feature finding process, including storage, RT transformation, and feature annotation.

Member Typedef Documentation

◆ ExternalChargeMap

typedef std::map<Int, ExternalRTMap> ExternalChargeMap

Charge to External RTMap mapping.

◆ ExternalPeptideMap

typedef std::map<AASequence, ExternalChargeMap> ExternalPeptideMap

Sequence to External Charge Map mapping.

◆ ExternalRTMap

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

RTMap for external data structure storage.

Constructor & Destructor Documentation

◆ FFIDAlgoExternalIDHandler()

FFIDAlgoExternalIDHandler ( )

Default constructor.

Member Function Documentation

◆ addDummyPeptideID_()

void addDummyPeptideID_	(	Feature &	feature,
		const PeptideIdentification *	ext_id
	)

private

Add dummy peptide identification from external data.

◆ addExternalPeptide()

void addExternalPeptide ( PeptideIdentification & peptide )

Add an external peptide to the handler's map.

◆ addExternalPeptideToMap_()

void addExternalPeptideToMap_	(	PeptideIdentification &	peptide,
		std::map< AASequence, std::map< Int, std::pair< std::multimap< double, PeptideIdentification * >, std::multimap< double, PeptideIdentification * >>>> &	peptide_map
	)

private

Add external peptide to charge map (merged version for compatibility)

◆ adjustFDRForExternalFeatures_()

void adjustFDRForExternalFeatures_	(	std::vector< double > &	fdr_probs,
		std::vector< double > &	fdr_qvalues,
		Size	n_internal_features
	)

private

Adjust FDR calculation for external features.

◆ alignInternalAndExternalIDs()

double alignInternalAndExternalIDs	(	const std::vector< PeptideIdentification > &	peptides_internal,
		const std::vector< PeptideIdentification > &	peptides_external,
		double	rt_quantile
	)

Align internal and external IDs to estimate RT shifts and return RT uncertainty.

◆ annotateFeatureWithExternalIDs_()

void annotateFeatureWithExternalIDs_ ( Feature & feature )

private

Check and set feature class based on external data.

◆ calculateFDR()

void calculateFDR ( FeatureMap & features )

Calculate FDR for classified features.

◆ checkNumObservations_()

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

private

Check observation counts for SVM.

◆ classifyFeaturesWithSVM()

void classifyFeaturesWithSVM	(	FeatureMap &	features,
		const Param &	param
	)

Classify features using SVM.

◆ fillExternalRTMap_()

bool fillExternalRTMap_	(	const AASequence &	sequence,
		Int	charge,
		std::multimap< double, PeptideIdentification * > &	rt_map
	)

private

Fill an external RTMap from our data for a specific peptide and charge.

◆ filterClassifiedFeatures()

void filterClassifiedFeatures	(	FeatureMap &	features,
		double	quality_cutoff
	)

Filter classified features.

◆ finalizeAssayFeatures_()

void finalizeAssayFeatures_	(	Feature &	best_feature,
		double	best_quality,
		double	quality_cutoff
	)

private

Finalize assay features.

◆ getRandomSample_()

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

private

Get random sample for SVM training.

◆ getRTTransformation()

const TransformationDescription& getRTTransformation ( ) const

Get the RT transformation.

◆ getSVMProbsInternal()

const std::map<double, std::pair<Size, Size> >& getSVMProbsInternal ( ) const

Get SVM probabilities for internal features.

◆ getUnbiasedSample_()

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

private

Get unbiased sample for SVM training.

◆ handleExternalFeature_()

void handleExternalFeature_	(	Feature &	feature,
		double	prob_positive,
		double	quality_cutoff
	)

private

Handle external feature probability.

◆ hasRTTransformation()

bool hasRTTransformation ( ) const

Check if we have RT transformation data.

◆ initSVMParameters_()

void initSVMParameters_ ( const Param & param )

private

Initialize SVM parameters.

◆ processExternalPeptides()

void processExternalPeptides ( std::vector< PeptideIdentification > & peptides_ext )

Process external peptide IDs.

◆ reset()

void reset ( )

Reset the handler's state.

◆ transformRT()

double transformRT ( double rt ) const

Transform RT from internal to external scale.

Member Data Documentation

◆ debug_level_

Int debug_level_

private

Debug level.

◆ external_peptide_map_

ExternalPeptideMap external_peptide_map_

private

External peptide storage.

◆ n_external_features_

Size n_external_features_

private

Number of external features.

◆ n_external_peptides_

Size n_external_peptides_

private

Number of external peptides.

◆ n_internal_features_

Size n_internal_features_

private

Number of internal features.

◆ rt_transformation_

TransformationDescription rt_transformation_

private

RT transformation description.

◆ svm_min_prob_

double svm_min_prob_

private

SVM minimum probability threshold.

◆ svm_n_parts_

Size svm_n_parts_

private

SVM number of parts for cross-validation.

◆ svm_n_samples_

Size svm_n_samples_

private

SVM number of samples for training.

◆ svm_predictor_names_

std::vector<String> svm_predictor_names_

private

SVM predictor names.

◆ svm_probs_external_

std::multiset<double> svm_probs_external_

private

SVM probabilities for external features.

◆ svm_probs_internal_

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

private

SVM probabilities for internal features.

◆ svm_quality_cutoff

double svm_quality_cutoff

private

SVM quality cutoff.

◆ svm_xval_out_

String svm_xval_out_

private

SVM cross-validation output file.

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ ExternalChargeMap

◆ ExternalPeptideMap

◆ ExternalRTMap

Constructor & Destructor Documentation

◆ FFIDAlgoExternalIDHandler()

Member Function Documentation

◆ addDummyPeptideID_()

◆ addExternalPeptide()

◆ addExternalPeptideToMap_()

◆ adjustFDRForExternalFeatures_()

◆ alignInternalAndExternalIDs()

◆ annotateFeatureWithExternalIDs_()

◆ calculateFDR()

◆ checkNumObservations_()

◆ classifyFeaturesWithSVM()

◆ fillExternalRTMap_()

◆ filterClassifiedFeatures()

◆ finalizeAssayFeatures_()

◆ getRandomSample_()

◆ getRTTransformation()

◆ getSVMProbsInternal()

◆ getUnbiasedSample_()

◆ handleExternalFeature_()

◆ hasRTTransformation()

◆ initSVMParameters_()

◆ processExternalPeptides()

◆ reset()

◆ transformRT()

Member Data Documentation

◆ debug_level_

◆ external_peptide_map_

◆ n_external_features_

◆ n_external_peptides_

◆ n_internal_features_

◆ rt_transformation_

◆ svm_min_prob_

◆ svm_n_parts_

◆ svm_n_samples_

◆ svm_predictor_names_

◆ svm_probs_external_

◆ svm_probs_internal_

◆ svm_quality_cutoff

◆ svm_xval_out_