FeatureFinderIdentificationAlgorithm Class Reference

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

Inheritance 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, std::vector< ProteinIdentification > proteins, std::vector< PeptideIdentification > peptides_ext, std::vector< ProteinIdentification > proteins_ext, FeatureMap &features)
void	runOnCandidates (FeatureMap &features)
PeakMap &	getMSData ()
const PeakMap &	getMSData () const
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...
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 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) const
	get regions in which peptide elutes (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)
void	postProcess_ (FeatureMap &features, bool with_external_ids)
void	statistics_ (const FeatureMap &features) const
	some statistics on detected features More...
void	createAssayLibrary_ (PeptideMap &peptide_map, PeptideRefRTMap &ref_rt_map)
void	addPeptideToMap_ (PeptideIdentification &peptide, PeptideMap &peptide_map, bool external=false) const
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, Int > &training_labels)
void	getRandomSample_ (std::map< Size, Int > &training_labels)
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)
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_
Size	n_external_peps_
double	rt_window_
double	mz_window_
bool	mz_window_ppm_
double	mapping_tolerance_
double	isotope_pmin_
Size	n_isotopes_
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_
Size	svm_n_samples_
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_
PeakMap	chrom_data_
TargetedExperiment	library_
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_
Size	n_external_features_
TransformationDescription	trafo_external_
	TransformationDescription trafo_; // RT transformation (to range 0-1) More...
std::map< String, double >	isotope_probs_
MRMFeatureFinderScoring	feat_finder_
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...

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

addPeptideRT_()

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

protected

addPeptideToMap_()

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

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

classifyFeatures_()

void classifyFeatures_ ( FeatureMap &  features )

protected

createAssayLibrary_()

void createAssayLibrary_ ( PeptideMap &  peptide_map, PeptideRefRTMap &  ref_rt_map  )

protected

ensureConvexHulls_()

void ensureConvexHulls_ ( Feature &  feature )

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 ( )

inline

getChromatograms() [2/2]

const PeakMap& getChromatograms ( ) const

inline

getLibrary() [1/2]

TargetedExperiment& getLibrary ( )

inline

getLibrary() [2/2]

const TargetedExperiment& getLibrary ( ) const

inline

getMSData() [1/2]

PeakMap& getMSData ( )

inline

getMSData() [2/2]

const PeakMap& getMSData ( ) const

inline

getProgressLogger() [1/2]

ProgressLogger& getProgressLogger ( )

inline

getProgressLogger() [2/2]

const ProgressLogger& getProgressLogger ( ) const

inline

getRandomSample_()

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

protected

getRTRegions_()

void getRTRegions_ ( ChargeMap &  peptide_data, std::vector< RTRegion > &  rt_regions  ) const

protected

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

getUnbiasedSample_()

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

protected

postProcess_()

void postProcess_ ( FeatureMap &  features, bool  with_external_ids  )

protected

run()

void run	(	std::vector< PeptideIdentification >	peptides,
		std::vector< ProteinIdentification >	proteins,
		std::vector< PeptideIdentification >	peptides_ext,
		std::vector< ProteinIdentification >	proteins_ext,
		FeatureMap &	features
	)

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.

runOnCandidates()

void runOnCandidates

(

FeatureMap &

features

)

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

candidates_out_

String candidates_out_

protected

chrom_data_

PeakMap chrom_data_

protected

debug_level_

Size debug_level_

protected

elution_model_

String elution_model_

protected

feat_finder_

MRMFeatureFinderScoring feat_finder_

protected

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

isotope_probs_

std::map<String, double> isotope_probs_

protected

library_

TargetedExperiment library_

protected

mapping_tolerance_

double mapping_tolerance_

protected

min_peak_width_

double min_peak_width_

protected

ms_data_

PeakMap ms_data_

protected

mz_window_

double mz_window_

protected

mz_window_ppm_

bool mz_window_ppm_

protected

n_external_features_

Size n_external_features_

protected

n_external_peps_

Size n_external_peps_

protected

n_internal_features_

Size n_internal_features_

protected

n_internal_peps_

Size n_internal_peps_

protected

n_isotopes_

Size n_isotopes_

protected

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

rt_quantile_

double rt_quantile_

protected

rt_window_

double rt_window_

protected

signal_to_noise_

double signal_to_noise_

protected

svm_min_prob_

double svm_min_prob_

protected

svm_n_parts_

Size svm_n_parts_

protected

svm_n_samples_

Size svm_n_samples_

protected

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)