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	getPickedProteinScores_ (std::unordered_map< String, ScoreToTgtDecLabelPair > &picked_scores, const ProteinIdentification &id, const String &decoy_string, bool decoy_prefix)
	Fills the scores_labels vector from an ProteinIdentification `id` for picked protein FDR. I.e. it only takes the better of the two scores for each target-decoy pair (based on the accession after removal of the `decoy_prefix`. More...

static void	getPickedProteinGroupScores_ (const std::unordered_map< String, ScoreToTgtDecLabelPair > &picked_scores, ScoreToTgtDecLabelPairs &scores_labels, const std::vector< ProteinIdentification::ProteinGroup > &grps, const String &decoy_string, bool decoy_prefix)
	Fills the scores_labels vector from a vector of ProteinGroups `grps` for picked protein group FDR. More...

static std::pair< bool, String >	removeDecoyStringIfPresent_ (const String &acc, const String &decoy_string, bool decoy_prefix)
	removes the `decoy_string` from `acc` if present. Returns if string was removed and the new string. More...

static void	fillPeptideScoreMap_ (std::unordered_map< String, ScoreToTgtDecLabelPair > &seq_to_score_labels, std::vector< PeptideIdentification > const &ids)

static void	fillPeptideScoreMap_ (std::unordered_map< String, ScoreToTgtDecLabelPair > &seq_to_score_labels, ConsensusMap const &map, bool include_unassigned)

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

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

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

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

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

template<typename HitPredicate >
static void	getScores_ (ScoreToTgtDecLabelPairs &scores_labels, const PeptideHit &hit, HitPredicate &&fun)

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

template<class ... Args>
static void	getPeptideScoresFromMap_ (ScoreToTgtDecLabelPairs &scores_labels, const ConsensusMap &cmap, bool include_unassigned_peptides, Args &&... args)
	Helper for getting scores in ConsensusMaps. More...

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 >
static void	setScoresHigherWorse_ (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 IDType , class ... Args>
static void	setScoresHigherWorseAndRemoveDecoys_ (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 HitType >
static void	setScoreHigherWorse_ (const std::map< double, double > &scores_to_FDR, HitType &hit, const std::string &old_score_type)

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)

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

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...

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

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...

template<class ... Args>
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, Args &&... args)
	Helper for applying set Scores on ConsensusMaps. More...

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

static void	setPeptideScoresFromMap_ (std::unordered_map< String, ScoreToTgtDecLabelPair > const &seq_to_fdr, std::vector< PeptideIdentification > &ids, std::string const &score_type, bool keep_decoys)

static void	setPeptideScoresFromMap_ (std::unordered_map< String, ScoreToTgtDecLabelPair > const &seq_to_fdr, ConsensusMap &map, std::string const &score_type, bool keep_decoys, bool include_unassigned)

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_().

◆ fillPeptideScoreMap_() [1/2]

static void fillPeptideScoreMap_	(	std::unordered_map< String, ScoreToTgtDecLabelPair > &	seq_to_score_labels,
		ConsensusMap const &	map,
		bool	include_unassigned
	)

static

◆ fillPeptideScoreMap_() [2/2]

static void fillPeptideScoreMap_	(	std::unordered_map< String, ScoreToTgtDecLabelPair > &	seq_to_score_labels,
		std::vector< PeptideIdentification > const &	ids
	)

static

◆ getPeptideScoresFromMap_()

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

inlinestatic

Helper for getting scores in ConsensusMaps.

Todo:: allow FeatureMap?

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

◆ getPickedProteinGroupScores_()

static void getPickedProteinGroupScores_	(	const std::unordered_map< String, ScoreToTgtDecLabelPair > &	picked_scores,
		ScoreToTgtDecLabelPairs &	scores_labels,
		const std::vector< ProteinIdentification::ProteinGroup > &	grps,
		const String &	decoy_string,
		bool	decoy_prefix
	)

static

Fills the scores_labels vector from a vector of ProteinGroups grps for picked protein group FDR.

Todo:: describe more

Parameters

picked_scores	Target accessions to pairs of scores and target decoy labels (usually 1.0 for target and 0.0 for decoy) to be used for lookup.
scores_labels	Scores and target-decoy value for all groups that had at least one picked protein. Targets preferred.
grps	The groups to iterate over
decoy_string	The decoy string to remove before comparing accesions for pairs.
decoy_prefix	If the `decoy_string` is a prefix (true) or suffix.

◆ getPickedProteinScores_()

static void getPickedProteinScores_	(	std::unordered_map< String, ScoreToTgtDecLabelPair > &	picked_scores,
		const ProteinIdentification &	id,
		const String &	decoy_string,
		bool	decoy_prefix
	)

static

Fills the scores_labels vector from an ProteinIdentification id for picked protein FDR. I.e. it only takes the better of the two scores for each target-decoy pair (based on the accession after removal of the decoy_prefix.

Parameters

picked_scores	Target accessions to pairs of scores and target decoy labels (usually 1.0 for target and 0.0 for decoy) to be filled.
id	The hits to iterate over
decoy_string	The decoy string to remove before comparing accesions for pairs.
decoy_prefix	If the `decoy_string` is a prefix (true) or suffix.

◆ 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_().

◆ removeDecoyStringIfPresent_()

static std::pair<bool,String> removeDecoyStringIfPresent_	(	const String &	acc,
		const String &	decoy_string,
		bool	decoy_prefix
	)

static

removes the decoy_string from acc if present. Returns if string was removed and the new string.

◆ setPeptideScoresForMap_()

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,
		Args &&...	args
	)

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
include_unassigned_peptides	Also modify unassigned peptide IDs in `cmap`?
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_().

◆ setPeptideScoresFromMap_() [1/2]

static void setPeptideScoresFromMap_	(	std::unordered_map< String, ScoreToTgtDecLabelPair > const &	seq_to_fdr,
		ConsensusMap &	map,
		std::string const &	score_type,
		bool	keep_decoys,
		bool	include_unassigned
	)

static

◆ setPeptideScoresFromMap_() [2/2]

static void setPeptideScoresFromMap_	(	std::unordered_map< String, ScoreToTgtDecLabelPair > const &	seq_to_fdr,
		std::vector< PeptideIdentification > &	ids,
		std::string const &	score_type,
		bool	keep_decoys
	)

static

◆ 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().

◆ setScoreHigherWorseAndMoveIfTarget_()

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

inlinestatic

Referenced by IDScoreGetterSetter::setScoresHigherWorseAndRemoveDecoys_().

Classes

Static Public Member Functions

Detailed Description

Member Function Documentation

◆ checkTDAnnotation_()

◆ fillPeptideScoreMap_() [1/2]

◆ fillPeptideScoreMap_() [2/2]

◆ getPeptideScoresFromMap_()

◆ getPickedProteinGroupScores_()

◆ getPickedProteinScores_()

◆ getTDLabel_()

◆ removeDecoyStringIfPresent_()

◆ setPeptideScoresForMap_()

◆ setPeptideScoresFromMap_() [1/2]

◆ setPeptideScoresFromMap_() [2/2]

◆ setScoreAndMoveIfTarget_() [1/2]

◆ setScoreAndMoveIfTarget_() [2/2]

◆ setScoreHigherWorseAndMoveIfTarget_()