A class for extracting and reinserting IDScores from Peptide/ProteinIdentifications and from ConsensusMaps. More...

#include <OpenMS/ANALYSIS/ID/IDScoreGetterSetter.h>

Classes
struct	IsHitType

struct	IsIDType

Static Public Member Functions
static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const std::vector< ProteinIdentification::ProteinGroup > &grps, const std::unordered_set< std::string > &decoy_accs)

static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const ProteinIdentification &id)

static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const PeptideIdentification &id, bool all_hits, int charge, const String &identifier)

static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const PeptideIdentification &id, bool all_hits, const String &identifier)

static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const PeptideIdentification &id, int charge, const String &identifier)

template<typename IDType , typename std::enable_if< IsIDType< IDType >::value >::type * = nullptr>
static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const IDType &id, const String &identifier)

template<class ... Args>
static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const PeptideIdentification &id, bool all_hits, Args &&... args)

static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const PeptideHit &hit, int charge)

static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const PeptideIdentification &id, int charge)

template<typename HitType , typename std::enable_if< IsHitType< HitType >::value >::type * = nullptr>
static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const HitType &hit)

template<typename IDType , typename std::enable_if< IsIDType< IDType >::value >::type * = nullptr>
static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const IDType &id)

template<class ... Args>
static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const std::vector< PeptideIdentification > &ids, Args &&... args)

static void	getPeptideScoresFromMap_ (ScoreToTgtDecLabelPairs &scores_labels, const ConsensusMap &cmap, bool include_unassigned_peptides)
	Helper for getting scores in ConsensusMaps. More...

static void	getPeptideScoresFromMap_ (ScoreToTgtDecLabelPairs &scores_labels, const ConsensusMap &cmap, bool include_unassigned_peptides, int charge)

static void	getPeptideScoresFromMap_ (ScoreToTgtDecLabelPairs &scores_labels, const ConsensusMap &cmap, bool include_unassigned_peptides, const String &identifier)

static void	getPeptideScoresFromMap_ (ScoreToTgtDecLabelPairs &scores_labels, const ConsensusMap &cmap, bool include_unassigned_peptides, int charge, const String &identifier)

static void	getPeptideScoresFromMap_ (ScoreToTgtDecLabelPairs &scores_labels, const ConsensusMap &cmap, bool include_unassigned_peptides, bool all_hits)

static void	getPeptideScoresFromMap_ (ScoreToTgtDecLabelPairs &scores_labels, const ConsensusMap &cmap, bool include_unassigned_peptides, bool all_hits, int charge)

static void	getPeptideScoresFromMap_ (ScoreToTgtDecLabelPairs &scores_labels, const ConsensusMap &cmap, bool include_unassigned_peptides, bool all_hits, const String &identifier)

static void	getPeptideScoresFromMap_ (ScoreToTgtDecLabelPairs &scores_labels, const ConsensusMap &cmap, bool include_unassigned_peptides, bool all_hits, int charge, const String &identifier)

static bool	getTDLabel_ (const MetaInfoInterface &idOrHit)
	For peptide hits, a hit is considered target also if it maps to both a target and a decoy protein (i.e. "target+decoy") as value in the "target_decoy" metavalue e.g. annotated by PeptideIndexer. More...

template<typename IDType , class ... Args>
static void	setScores_ (const std::map< double, double > &scores_to_FDR, std::vector< IDType > &ids, const std::string &score_type, bool higher_better, Args &... args)

template<typename IDType >
static String	setScoreType_ (IDType &id, const std::string &score_type, bool higher_better)

template<typename IDType >
static void	setScores_ (const std::map< double, double > &scores_to_FDR, IDType &id, const std::string &score_type, bool higher_better, bool keep_decoy)

template<typename IDType >
static void	setScores_ (const std::map< double, double > &scores_to_FDR, IDType &id, const String &old_score_type)

template<typename IDType , class ... Args>
static void	setScoresAndRemoveDecoys_ (const std::map< double, double > &scores_to_FDR, IDType &id, const String &old_score_type, Args ... args)

template<typename HitType >
static void	setScore_ (const std::map< double, double > &scores_to_FDR, HitType &hit, const std::string &old_score_type)

template<typename IDType >
static void	setScores_ (const std::map< double, double > &scores_to_FDR, IDType &id, const std::string &score_type, bool higher_better)

static void	setScores_ (const std::map< double, double > &scores_to_FDR, PeptideIdentification &id, const std::string &score_type, bool higher_better, bool keep_decoy, int charge)

static void	setScores_ (const std::map< double, double > &scores_to_FDR, PeptideIdentification &id, const std::string &score_type, bool higher_better, bool keep_decoy, int charge, const String &identifier)

template<typename IDType >
static void	setScores_ (const std::map< double, double > &scores_to_FDR, IDType &id, const std::string &score_type, bool higher_better, bool keep_decoy, const String &identifier)

static void	setScores_ (const std::map< double, double > &scores_to_FDR, PeptideIdentification &id, const std::string &score_type, bool higher_better, int charge, const String &identifier)

template<typename IDType >
static void	setScores_ (const std::map< double, double > &scores_to_FDR, IDType &id, const std::string &score_type, bool higher_better, const String &identifier)

static void	setScores_ (const std::map< double, double > &scores_to_FDR, std::vector< ProteinIdentification::ProteinGroup > &grps, const std::string &score_type, bool higher_better)

template<typename HitType >
static void	setScoreAndMoveIfTarget_ (const std::map< double, double > &scores_to_FDR, HitType &hit, const std::string &old_score_type, std::vector< HitType > &new_hits)
	Used when keep_decoy_peptides or proteins is false. More...

static void	setScoreAndMoveIfTarget_ (const std::map< double, double > &scores_to_FDR, PeptideHit &hit, const std::string &old_score_type, std::vector< PeptideHit > &new_hits, int charge)
	Used when keep_decoy_peptides is false and charge states are considered. More...

static void	setPeptideScoresForMap_ (const std::map< double, double > &scores_to_FDR, ConsensusMap &cmap, bool include_unassigned_peptides, const std::string &score_type, bool higher_better, bool keep_decoy)
	Helper for applying set Scores on ConsensusMaps. More...

static void	setPeptideScoresForMap_ (const std::map< double, double > &scores_to_FDR, ConsensusMap &cmap, bool include_unassigned_peptides, const std::string &score_type, bool higher_better, bool keep_decoy, int charge)

static void	setPeptideScoresForMap_ (const std::map< double, double > &scores_to_FDR, ConsensusMap &cmap, bool include_unassigned_peptides, const std::string &score_type, bool higher_better, bool keep_decoy, const String &run_identifier)

static void	setPeptideScoresForMap_ (const std::map< double, double > &scores_to_FDR, ConsensusMap &cmap, bool include_unassigned_peptides, const std::string &score_type, bool higher_better, bool keep_decoy, int charge, const String &run_identifier)

static void	checkTDAnnotation_ (const MetaInfoInterface &id_or_hit)
	To check the metavalues before we do anything. More...

Detailed Description

A class for extracting and reinserting IDScores from Peptide/ProteinIdentifications and from ConsensusMaps.

Member Function Documentation

◆ checkTDAnnotation_()

static void checkTDAnnotation_ ( const MetaInfoInterface & id_or_hit )

inlinestatic

To check the metavalues before we do anything.

Parameters

id_or_hit Any Object with MetaInfoInterface. Specifically ID or Hit Type here.

Exceptions

Exception::MissingInformation if target_decoy annotation does not exist

References MetaInfoInterface::metaValueExists().

Referenced by IDScoreGetterSetter::getScores_().

◆ getPeptideScoresFromMap_() [1/8]

static void getPeptideScoresFromMap_	(	ScoreToTgtDecLabelPairs &	scores_labels,
		const ConsensusMap &	cmap,
		bool	include_unassigned_peptides
	)

inlinestatic

Helper for getting scores in ConsensusMaps.

Todo:: allow FeatureMap?

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), and IDScoreGetterSetter::getScores_().

◆ getPeptideScoresFromMap_() [2/8]

static void getPeptideScoresFromMap_	(	ScoreToTgtDecLabelPairs &	scores_labels,
		const ConsensusMap &	cmap,
		bool	include_unassigned_peptides,
		bool	all_hits
	)

inlinestatic

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), and IDScoreGetterSetter::getScores_().

◆ getPeptideScoresFromMap_() [3/8]

static void getPeptideScoresFromMap_	(	ScoreToTgtDecLabelPairs &	scores_labels,
		const ConsensusMap &	cmap,
		bool	include_unassigned_peptides,
		bool	all_hits,
		const String &	identifier
	)

inlinestatic

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), and IDScoreGetterSetter::getScores_().

◆ getPeptideScoresFromMap_() [4/8]

static void getPeptideScoresFromMap_	(	ScoreToTgtDecLabelPairs &	scores_labels,
		const ConsensusMap &	cmap,
		bool	include_unassigned_peptides,
		bool	all_hits,
		int	charge
	)

inlinestatic

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), and IDScoreGetterSetter::getScores_().

◆ getPeptideScoresFromMap_() [5/8]

static void getPeptideScoresFromMap_	(	ScoreToTgtDecLabelPairs &	scores_labels,
		const ConsensusMap &	cmap,
		bool	include_unassigned_peptides,
		bool	all_hits,
		int	charge,
		const String &	identifier
	)

inlinestatic

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), and IDScoreGetterSetter::getScores_().

◆ getPeptideScoresFromMap_() [6/8]

static void getPeptideScoresFromMap_	(	ScoreToTgtDecLabelPairs &	scores_labels,
		const ConsensusMap &	cmap,
		bool	include_unassigned_peptides,
		const String &	identifier
	)

inlinestatic

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), and IDScoreGetterSetter::getScores_().

◆ getPeptideScoresFromMap_() [7/8]

static void getPeptideScoresFromMap_	(	ScoreToTgtDecLabelPairs &	scores_labels,
		const ConsensusMap &	cmap,
		bool	include_unassigned_peptides,
		int	charge
	)

inlinestatic

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), and IDScoreGetterSetter::getScores_().

◆ getPeptideScoresFromMap_() [8/8]

static void getPeptideScoresFromMap_	(	ScoreToTgtDecLabelPairs &	scores_labels,
		const ConsensusMap &	cmap,
		bool	include_unassigned_peptides,
		int	charge,
		const String &	identifier
	)

inlinestatic

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), and IDScoreGetterSetter::getScores_().

◆ getTDLabel_()

static bool getTDLabel_ ( const MetaInfoInterface & idOrHit )

inlinestatic

For peptide hits, a hit is considered target also if it maps to both a target and a decoy protein (i.e. "target+decoy") as value in the "target_decoy" metavalue e.g. annotated by PeptideIndexer.

References MetaInfoInterface::getMetaValue().

Referenced by IDScoreGetterSetter::getScores_().

◆ setPeptideScoresForMap_() [1/4]

static void setPeptideScoresForMap_	(	const std::map< double, double > &	scores_to_FDR,
		ConsensusMap &	cmap,
		bool	include_unassigned_peptides,
		const std::string &	score_type,
		bool	higher_better,
		bool	keep_decoy
	)

inlinestatic

Helper for applying set Scores on ConsensusMaps.

Template Parameters

Args	optional additional arguments (charge, run ID)

Parameters

scores_to_FDR	maps original scores to FDR
cmap	the ConsensusMap
score_type	FDR or q-Value
higher_better	usually false
keep_decoy	read from Param object
args	optional additional arguments (int charge, string run ID)

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), and IDScoreGetterSetter::setScores_().

◆ setPeptideScoresForMap_() [2/4]

static void setPeptideScoresForMap_	(	const std::map< double, double > &	scores_to_FDR,
		ConsensusMap &	cmap,
		bool	include_unassigned_peptides,
		const std::string &	score_type,
		bool	higher_better,
		bool	keep_decoy,
		const String &	run_identifier
	)

inlinestatic

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), and IDScoreGetterSetter::setScores_().

◆ setPeptideScoresForMap_() [3/4]

static void setPeptideScoresForMap_	(	const std::map< double, double > &	scores_to_FDR,
		ConsensusMap &	cmap,
		bool	include_unassigned_peptides,
		const std::string &	score_type,
		bool	higher_better,
		bool	keep_decoy,
		int	charge
	)

inlinestatic

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), and IDScoreGetterSetter::setScores_().

◆ setPeptideScoresForMap_() [4/4]

static void setPeptideScoresForMap_	(	const std::map< double, double > &	scores_to_FDR,
		ConsensusMap &	cmap,
		bool	include_unassigned_peptides,
		const std::string &	score_type,
		bool	higher_better,
		bool	keep_decoy,
		int	charge,
		const String &	run_identifier
	)

inlinestatic

References MapUtilities< MapType >::applyFunctionOnPeptideIDs(), and IDScoreGetterSetter::setScores_().

◆ setScoreAndMoveIfTarget_() [1/2]

static void setScoreAndMoveIfTarget_	(	const std::map< double, double > &	scores_to_FDR,
		HitType &	hit,
		const std::string &	old_score_type,
		std::vector< HitType > &	new_hits
	)

inlinestatic

Used when keep_decoy_peptides or proteins is false.

Template Parameters

HitType ProteinHit or PeptideHit

Parameters

scores_to_FDR	map from original score to FDR/qVal
hit	The hit (moved to `new_hits` if its a target hit)
old_score_type	to save it in metavalue
new_hits	where to move if target (i.e. target or target+decoy)

Referenced by IDScoreGetterSetter::setScoresAndRemoveDecoys_().

◆ setScoreAndMoveIfTarget_() [2/2]

static void setScoreAndMoveIfTarget_	(	const std::map< double, double > &	scores_to_FDR,
		PeptideHit &	hit,
		const std::string &	old_score_type,
		std::vector< PeptideHit > &	new_hits,
		int	charge
	)

inlinestatic

Used when keep_decoy_peptides is false and charge states are considered.

Parameters

scores_to_FDR	map from original score to FDR/qVal
hit	the PeptideHit itself
old_score_type	to save it in metavalue
new_hits	where to move if target (i.e. target or target+decoy)
charge	If only peptides with charge X are currently considered

References PeptideHit::getCharge(), MetaInfoInterface::getMetaValue(), PeptideHit::getScore(), MetaInfoInterface::setMetaValue(), and PeptideHit::setScore().

Classes

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ checkTDAnnotation_()

◆ getPeptideScoresFromMap_() [1/8]

◆ getPeptideScoresFromMap_() [2/8]

◆ getPeptideScoresFromMap_() [3/8]

◆ getPeptideScoresFromMap_() [4/8]

◆ getPeptideScoresFromMap_() [5/8]

◆ getPeptideScoresFromMap_() [6/8]

◆ getPeptideScoresFromMap_() [7/8]

◆ getPeptideScoresFromMap_() [8/8]

◆ getTDLabel_()

◆ setPeptideScoresForMap_() [1/4]

◆ setPeptideScoresForMap_() [2/4]

◆ setPeptideScoresForMap_() [3/4]

◆ setPeptideScoresForMap_() [4/4]

◆ setScoreAndMoveIfTarget_() [1/2]

◆ setScoreAndMoveIfTarget_() [2/2]