ID-guided MS1 feature finder; the algorithm behind FeatureFinderIdentification. More...

#include <OpenMS/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	IMStats
	Ion mobility statistics for a peptide in a specific RT region and charge state. 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; installs the FFid parameters (see class docs)

void	run (PeptideIdentificationList peptides, const std::vector< ProteinIdentification > &proteins, PeptideIdentificationList peptides_ext, std::vector< ProteinIdentification > proteins_ext, FeatureMap &features, const FeatureMap &seeds=FeatureMap(), const std::string &spectra_file="")
	Run the FFid pipeline; for FAIMS data this dispatches one run per CV group and merges results.

void	runOnCandidates (FeatureMap &features)
	Re-score / filter an existing candidate FeatureMap in place using the configured classifier and quality cutoffs (entry point used to re-process candidates exported via the `candidates_out` parameter).

PeakMap &	getMSData ()
	Mutable access to the cached MS1 data.

const PeakMap &	getMSData () const
	Read-only access to the cached MS1 data.

void	setMSData (const PeakMap &ms_data)
	Copy the MS data into the algorithm instance; useful from pyOpenMS where moving is awkward.

void	setMSData (PeakMap &&ms_data)
	Move the MS data into the algorithm instance (no copy).

PeakMap &	getChromatograms ()
	Mutable access to the accumulated extracted chromatograms (XICs) from the last run.

const PeakMap &	getChromatograms () const
	Read-only access to the accumulated extracted chromatograms.

ProgressLogger &	getProgressLogger ()
	Mutable access to the progress logger used by the algorithm.

const ProgressLogger &	getProgressLogger () const
	Read-only access to the progress logger.

TargetedExperiment &	getLibrary ()
	Mutable access to the assay library used / produced by the last run.

const TargetedExperiment &	getLibrary () const
	Read-only access to the assay library used / produced by the last run.

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

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.

virtual	~DefaultParamHandler ()
	Destructor.

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

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

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

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

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

const std::string &	getName () const
	Non-mutable access to the name.

void	setName (const std::string &name)
	Mutable access to the name.

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

Protected Types
typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace	MassTrace

typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces	MassTraces

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

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

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

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

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

void	generateTransitions_ (const std::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:

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

IMStats	getRTRegionIMStats_ (const RTRegion &r)
	Calculate ion mobility statistics for peptide identifications in an RT region.

void	calculateGlobalIMStats_ ()
	Calculate global IM statistics from MS data and peptide identifications.

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.

void	ensureConvexHulls_ (Feature &feature) const

void	postProcess_ (FeatureMap &features, bool with_external_ids)

void	validateSVMParameters_ () const
	Helper functions for run()

void	initializeFeatureFinder_ ()

double	calculateRTWindow_ (double rt_uncertainty) const

void	removeSeedPseudoIDs_ (FeatureMap &features)

std::pair< double, double >	calculateRTBounds_ (double rt_min, double rt_max) const
	Calculate RT bounds with optional tolerance expansion.

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

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	filterFeatures_ (FeatureMap &features, bool classified)

void	runSingleGroup_ (PeptideIdentificationList peptides, const std::vector< ProteinIdentification > &proteins, PeptideIdentificationList peptides_ext, std::vector< ProteinIdentification > proteins_ext, FeatureMap &features, const FeatureMap &seeds, const std::string &spectra_file)

Size	addSeeds_ (PeptideIdentificationList &peptides, const FeatureMap &seeds)

Size	addOffsetPeptides_ (PeptideIdentificationList &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.

Static Protected Member Functions
static bool	isSeedPseudoHit_ (const PeptideHit &hit)
	Helper function to check if a peptide hit is a seed pseudo-ID.

Protected Attributes
PeptideMap	peptide_map_

Size	n_internal_peps_
	number of internal peptide

Size	n_external_peps_
	number of external peptides

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

double	rt_window_
	RT window width.

double	mz_window_
	m/z window width

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

double	mapping_tolerance_
	RT tolerance for mapping IDs to features.

double	isotope_pmin_
	min. isotope probability for peptide assay

Size	n_isotopes_
	number of isotopes for peptide assay

double	rt_quantile_

double	peak_width_

double	min_peak_width_

double	signal_to_noise_

std::string	elution_model_

double	svm_min_prob_

StringList	svm_predictor_names_

std::string	svm_xval_out_

double	svm_quality_cutoff

Size	svm_n_parts_
	number of partitions for SVM cross-validation

Size	svm_n_samples_
	number of samples for SVM training

std::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

PeakMap	chrom_data_
	accumulated chromatograms (XICs)

TargetedExperiment	library_
	assays for peptides (cleared per chunk during processing)

TargetedExperiment	output_library_
	accumulated assays for output (populated from library_ before clearing)

bool	quantify_decoys_

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

double	seed_apex_rt_tolerance_ {5.0}
	max allowed RT deviation (s) between seed apex and detected feature apex; seed-derived features exceeding this are removed (0 = disabled)

bool	use_psm_cutoff_

double	psm_score_cutoff_

PeptideIdentificationList	unassignedIDs_

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

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

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

Size	n_internal_features_
	internal feature counter (for FDR calculation)

Size	n_external_features_

std::map< std::string, double >	isotope_probs_
	TransformationDescription trafo_; // RT transformation (to range 0-1)

std::map< std::string, IMStats >	im_stats_
	Ion mobility statistics per peptide reference (peptide sequence/charge:region)

IMStats	global_im_stats_
	Global ion mobility statistics from all peptide identifications.

MRMFeatureFinderScoring	feat_finder_
	OpenSWATH feature finder.

Internal::FFIDAlgoExternalIDHandler	external_id_handler_
	Handler for external peptide IDs.

ProgressLogger	prog_log_

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

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

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

std::string	error_name_
	Name that is displayed in error messages during the parameter checking.

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

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

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

Detailed Description

ID-guided MS1 feature finder; the algorithm behind FeatureFinderIdentification.

Uses peptide identifications as targets to drive chromatogram extraction from MS1 data, builds a per-peptide assay library on the fly, scores extracted peak groups with MRMFeatureFinderScoring, and emits a FeatureMap of quantified features.

Inputs

Two ID layers are accepted:

Internal IDs (peptides / proteins) — the high-confidence anchors used to define candidate elution windows and to train the SVM classifier (when classification is enabled).
External IDs (peptides_ext / proteins_ext) — optional, lower-confidence transfer IDs (e.g. from match-between-runs) used to extend the search space without contributing to SVM training. When external lists are empty, the algorithm skips machine learning and FDR estimation entirely.

Optional seeds from an upstream untargeted feature finder can also be added.

FAIMS handling

If the input PeakMap carries multiple FAIMS compensation voltages, run splits the data via IMDataConverter::splitByFAIMSCV, runs the per-CV pipeline in a fresh algorithm instance per group (peptide IDs filtered by FAIMS_CV through FAIMSHelper::filterPeptidesByFAIMSCV), annotates the resulting features with the FAIMS_CV meta value, and merges everything back into the caller's features. IDs without a FAIMS_CV are processed against every CV group for backward compatibility. In the multi-FAIMS case, getLibrary returns an empty library because each CV group has its own assay library.

ID-list transformations inside run()

Both ID lists are taken by value (see the run() signature), so the caller's containers are never observably modified. The transformations described here happen on the function's local copies and influence which IDs reach features:

The local copy of peptides is shrunk to the best hit per identification.
FFid meta values are added to each surviving hit before it is written into features.
If seeds carries IDs, those are appended to the local copy of peptides before scoring.

Primary MS-run path

After feature detection the FeatureMap's primaryMSRunPath is set to the ms_data_'s recorded run path; if that is not a valid / readable mzML, spectra_file is used as a fallback annotation (see MSExperiment overload of FeatureMap::setPrimaryMSRunPath).

Class Documentation

◆ OpenMS::FeatureFinderIdentificationAlgorithm::IMStats

struct OpenMS::FeatureFinderIdentificationAlgorithm::IMStats

Ion mobility statistics for a peptide in a specific RT region and charge state.

This structure stores statistical measures of ion mobility values collected from peptide identifications within a single RT region. These statistics are used for:

Chromatogram extraction with appropriate IM windows (using median)
Feature annotation for quality control (all three values)
Detecting potential mis-identifications (large min-max spread may indicate issues)

All values default to -1.0 to indicate missing/unavailable IM data.

Collaboration diagram for FeatureFinderIdentificationAlgorithm::IMStats:

[legend]

Class Members
double	max = -1.0	Maximum IM value (upper bound of IM distribution)
double	median = -1.0	Median IM value (robust central tendency, used for extraction)
double	min = -1.0	Minimum IM value (lower bound of IM distribution)

◆ 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<std::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; installs the FFid parameters (see class docs)

Member Function Documentation

◆ addOffsetPeptides_()

Size addOffsetPeptides_	(	PeptideIdentificationList &	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_	(	PeptideIdentificationList &	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

◆ calculateGlobalIMStats_()

void calculateGlobalIMStats_ ( )

protected

Calculate global IM statistics from MS data and peptide identifications.

Uses MSExperiment::getMinMobility()/getMaxMobility() to get the full IM range from raw data (min/max), and calculates median from peptide identifications for robust central tendency. Must be called BEFORE addSeeds_() to ensure global statistics are based only on identified peptides.

Seeds may or may not have IM annotation depending on the feature finder. Seeds with IM annotation use their own IM value; seeds without IM are extracted across the full IM range of the dataset.

◆ calculateRTBounds_()

std::pair< double, double > calculateRTBounds_	(	double	rt_min,
		double	rt_max
	)		const

protected

Calculate RT bounds with optional tolerance expansion.

◆ calculateRTWindow_()

double calculateRTWindow_ ( double rt_uncertainty ) const

protected

◆ chunk_()

template<typename It >

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.

◆ 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 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

◆ generateTransitions_()

void generateTransitions_	(	const std::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 ( )

Mutable access to the accumulated extracted chromatograms (XICs) from the last run.

Returns: Reference to the accumulated XIC PeakMap.

◆ getChromatograms() [2/2]

const PeakMap & getChromatograms ( ) const

Read-only access to the accumulated extracted chromatograms.

Returns: Const reference to the accumulated XIC PeakMap.

◆ getLibrary() [1/2]

TargetedExperiment & getLibrary ( )

Mutable access to the assay library used / produced by the last run.

Returns: Reference to the TargetedExperiment library.

Note: For multi-FAIMS inputs this returns an empty library because each CV group has its own internal library.

◆ getLibrary() [2/2]

const TargetedExperiment & getLibrary ( ) const

Read-only access to the assay library used / produced by the last run.

Returns: Const reference to the TargetedExperiment library (empty for multi-FAIMS inputs — see the non-const overload).

◆ getMSData() [1/2]

PeakMap & getMSData ( )

Mutable access to the cached MS1 data.

Returns: Reference to the cached PeakMap (already pre-processed by run when called after run()).

Referenced by NuXLRTPrediction::train().

◆ getMSData() [2/2]

const PeakMap & getMSData ( ) const

Read-only access to the cached MS1 data.

Returns: Const reference to the cached PeakMap.

◆ getProgressLogger() [1/2]

ProgressLogger & getProgressLogger ( )

Mutable access to the progress logger used by the algorithm.

Returns: Reference to the ProgressLogger (configure log type, etc.).

◆ getProgressLogger() [2/2]

const ProgressLogger & getProgressLogger ( ) const

Read-only access to the progress logger.

Returns: Const reference to the ProgressLogger.

◆ getRTRegionIMStats_()

IMStats getRTRegionIMStats_ ( const RTRegion & r )

protected

Calculate ion mobility statistics for peptide identifications in an RT region.

Computes median, min, and max IM values from peptide identifications within the given RT region (across all charge states). Individual IDs lacking IM annotation are skipped (with warning), and statistics are calculated from the remaining IDs with valid IM data. The median is used for robust central tendency estimation and is more resistant to outliers than the mean.

Seeds from untargeted feature finders may or may not have an IM meta value set, depending on the feature finder. If IM is annotated on the seed, it is used for targeted extraction. If not, the seed is extracted across the full IM range (ChromatogramExtractor disables IM filtering when ion_mobility < 0).

Note: RT region boundaries are determined from ALL IDs (including those without IM), so this only affects IM statistics calculation, not RT extraction.

Parameters

[in] r RT region containing peptide identifications grouped by charge state

Returns: IMStats structure with median/min/max, or {-1, -1, -1} if no valid IM data

See also: IMStats for details on the returned structure

◆ 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

◆ initializeFeatureFinder_()

void initializeFeatureFinder_ ( )

protected

◆ isSeedPseudoHit_()

static bool isSeedPseudoHit_ ( const PeptideHit & hit )

staticprotected

Helper function to check if a peptide hit is a seed pseudo-ID.

◆ postProcess_()

void postProcess_	(	FeatureMap &	features,
		bool	with_external_ids
	)

protected

◆ removeSeedPseudoIDs_()

void removeSeedPseudoIDs_ ( FeatureMap & features )

protected

◆ run()

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

Run the FFid pipeline; for FAIMS data this dispatches one run per CV group and merges results.

See the class brief for the role of external IDs, the seeds list, the FAIMS handling, the side effects on the input ID lists, and the primary-MS-run-path fallback semantics.

Parameters

[in]	peptides	Internal peptide IDs (taken by value). The local copy is shrunk to best hit per identification and FFid meta values are added before being written into `features`; the caller's container is not modified.
[in]	proteins	Protein IDs corresponding to `peptides`.
[in]	peptides_ext	External peptide IDs, optional (may be empty); taken by value with the same shrink-and-annotate treatment as `peptides`.
[in]	proteins_ext	Protein IDs corresponding to `peptides_ext`.
[out]	features	Quantified feature map; pre-existing contents are cleared for FAIMS data and replaced.
[in]	seeds	Optional pre-detected features from an untargeted feature finder.
[in]	spectra_file	Source mzML path used as a fallback for `primaryMSRunPath` annotation when the MSExperiment's own path isn't usable.

Referenced by NuXLRTPrediction::train().

◆ runOnCandidates()

void runOnCandidates ( FeatureMap & features )

Re-score / filter an existing candidate FeatureMap in place using the configured classifier and quality cutoffs (entry point used to re-process candidates exported via the candidates_out parameter).

◆ runSingleGroup_()

void runSingleGroup_	(	PeptideIdentificationList	peptides,
		const std::vector< ProteinIdentification > &	proteins,
		PeptideIdentificationList	peptides_ext,
		std::vector< ProteinIdentification >	proteins_ext,
		FeatureMap &	features,
		const FeatureMap &	seeds,
		const std::string &	spectra_file
	)

protected

Core processing logic for a single (non-FAIMS or single FAIMS group) dataset Called by run() either directly or for each FAIMS CV group

◆ setMSData() [1/2]

void setMSData ( const PeakMap & ms_data )

Copy the MS data into the algorithm instance; useful from pyOpenMS where moving is awkward.

Parameters

[in] ms_data Source PeakMap; copied into the internal cache.

◆ setMSData() [2/2]

void setMSData ( PeakMap && ms_data )

Move the MS data into the algorithm instance (no copy).

Parameters

[in] ms_data Source PeakMap; moved into the internal cache. getMSData will later expose the cached (possibly preprocessed) copy, not the original.

◆ 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.

◆ validateSVMParameters_()

void validateSVMParameters_ ( ) const

protected

Helper functions for run()

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_

std::string candidates_out_

protected

◆ chrom_data_

PeakMap chrom_data_

protected

accumulated chromatograms (XICs)

◆ debug_level_

Size debug_level_

protected

◆ elution_model_

std::string elution_model_

protected

◆ external_id_handler_

Internal::FFIDAlgoExternalIDHandler external_id_handler_

protected

Handler for external peptide IDs.

◆ 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

◆ global_im_stats_

IMStats global_im_stats_

protected

Global ion mobility statistics from all peptide identifications.

Calculated from peptide identifications BEFORE seeds are added (ensuring we only learn from real IDs with IM annotation). Provides context for the typical IM range in the dataset.

◆ im_stats_

std::map<std::string, IMStats> im_stats_

protected

Ion mobility statistics per peptide reference (peptide sequence/charge:region)

Maps from full peptide reference (e.g., "PEPTIDE/2:1") to IM statistics. Populated during createAssayLibrary_() and used during annotateFeatures_() to add IM_median, IM_min, and IM_max meta-values to features.

◆ isotope_pmin_

double isotope_pmin_

protected

min. isotope probability for peptide assay

◆ isotope_probs_

std::map<std::string, double> isotope_probs_

protected

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

isotope probabilities of transitions

◆ library_

TargetedExperiment library_

protected

assays for peptides (cleared per chunk during processing)

◆ 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

◆ output_library_

TargetedExperiment output_library_

protected

accumulated assays for output (populated from library_ before clearing)

◆ 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_apex_rt_tolerance_

double seed_apex_rt_tolerance_ {5.0}

protected

max allowed RT deviation (s) between seed apex and detected feature apex; seed-derived features exceeding this are removed (0 = disabled)

◆ 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_

std::string svm_xval_out_

protected

◆ unassignedIDs_

PeptideIdentificationList unassignedIDs_

protected

◆ use_psm_cutoff_

bool use_psm_cutoff_

protected

Classes

Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Inputs

FAIMS handling

ID-list transformations inside run()

Primary MS-run path

Class Documentation

◆ OpenMS::FeatureFinderIdentificationAlgorithm::IMStats

◆ 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_()

◆ calculateGlobalIMStats_()

◆ calculateRTBounds_()

◆ calculateRTWindow_()

◆ chunk_()

◆ createAssayLibrary_()

◆ ensureConvexHulls_()

◆ filterFeatures_()

◆ 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]

◆ getRTRegionIMStats_()

◆ getRTRegions_()

◆ initializeFeatureFinder_()

◆ isSeedPseudoHit_()

◆ postProcess_()

◆ removeSeedPseudoIDs_()

◆ run()

◆ runOnCandidates()

◆ runSingleGroup_()

◆ setMSData() [1/2]

◆ setMSData() [2/2]

◆ statistics_()

◆ updateMembers_()

◆ validateSVMParameters_()

Member Data Documentation

◆ add_mass_offset_peptides_

◆ batch_size_

◆ candidates_out_

◆ chrom_data_

◆ debug_level_

◆ elution_model_

◆ external_id_handler_

◆ feat_finder_

◆ feature_compare_

◆ feature_filter_peptides_

◆ feature_filter_quality_

◆ global_im_stats_

◆ im_stats_

◆ isotope_pmin_

◆ isotope_probs_

◆ library_

◆ mapping_tolerance_

◆ min_peak_width_