Class for storing Percolator tab-delimited input files. More...

#include <OpenMS/FORMAT/PercolatorInfile.h>

Public Types
using	PinFeatureMetaValueMap = std::map< std::pair< size_t, size_t >, std::set< std::string > >
	PIN meta values added to each hit, keyed by (peptide ID index, hit index).

Static Public Member Functions
static void	store (const std::string &pin_file, const PeptideIdentificationList &peptide_ids, const StringList &feature_set, const std::string &enz, int min_charge, int max_charge)

static PeptideIdentificationList	load (const std::string &pin_file, bool higher_score_better, const std::string &score_name, const StringList &extra_scores, StringList &filenames, std::string decoy_prefix="", double threshold=0.01, bool SageAnnotation=false)
	Loads peptide identifications from a Percolator input file.

static std::string	getScanIdentifier (const PeptideIdentification &pid, size_t index)

static StringList	getStandardFeatureSet (int min_charge, int max_charge)
	Returns the standard Percolator feature columns every .pin file should declare.

static std::set< std::pair< size_t, size_t > >	stampPinFeaturesOnHits (PeptideIdentificationList &peptide_ids, const std::string &enz, int min_charge, int max_charge)
	Compute and stamp PIN-equivalent meta values on every PeptideHit.

static std::set< std::pair< size_t, size_t > >	stampPinFeaturesOnHits (PeptideIdentificationList &peptide_ids, const std::string &enz, int min_charge, int max_charge, PinFeatureMetaValueMap &added_meta_values)
	Compute and stamp PIN-equivalent meta values, recording newly added keys.

static double	getFeatureValue (const DataValue &value, const std::string &feature)
	Numeric value of a PIN feature, as the percolator executable reads it.

Static Protected Member Functions
static TextFile	preparePin_ (const PeptideIdentificationList &peptide_ids, const StringList &feature_set, const std::string &enz, int min_charge, int max_charge)

static bool	isEnz_ (const char &n, const char &c, const std::string &enz)

static Size	countEnzymatic_ (const std::string &peptide, const std::string &enz)

Detailed Description

Class for storing Percolator tab-delimited input files.

Member Typedef Documentation

◆ PinFeatureMetaValueMap

using PinFeatureMetaValueMap = std::map<std::pair<size_t, size_t>, std::set<std::string> >

PIN meta values added to each hit, keyed by (peptide ID index, hit index).

Member Function Documentation

◆ countEnzymatic_()

static Size countEnzymatic_	(	const std::string &	peptide,
		const std::string &	enz
	)

staticprotected

◆ getFeatureValue()

static double getFeatureValue	(	const DataValue &	value,
		const std::string &	feature
	)

static

Numeric value of a PIN feature, as the percolator executable reads it.

The .pin writer (store) prints every feature as text and the percolator executable parses that text as a number. So an integer or floating-point meta value counts as it is, and a string meta value counts as the number it spells: adapters that read search engine scores from text keep them as strings (e.g. SageAdapter, via load). In-process rescoring has to read feature values through this function to train on the same numbers as the executable; DataValue's conversion to double does not parse a string, it yields an unrelated number.

Parameters

[in]	value	Meta value of the feature
[in]	feature	Name of the feature (for the error message)

Returns: The numeric value

Exceptions

Exception::InvalidValue if value is empty, a list, a string that is not a number, or not finite (NaN, infinity); the executable rejects such a feature as well

◆ getScanIdentifier()

static std::string getScanIdentifier	(	const PeptideIdentification &	pid,
		size_t	index
	)

static

◆ getStandardFeatureSet()

static StringList getStandardFeatureSet	(	int	min_charge,
		int	max_charge
	)

static

Returns the standard Percolator feature columns every .pin file should declare.

The list contains the three mandatory header columns (SpecId, Label, ScanNr) followed by the standard per-PSM features that preparePin_ computes and sets on every hit: ExpMass, CalcMass, mass, peplen, charge{min..max}, enzN, enzC, enzInt, dm, absdm. Callers should append their search-engine-specific extra_features (and finally Peptide, Proteins) to this list before calling store. This is the single source of truth used by PercolatorAdapter and any other tool that emits .pin for external percolator consumption.

◆ isEnz_()

static bool isEnz_	(	const char &	n,
		const char &	c,
		const std::string &	enz
	)

staticprotected

◆ load()

static PeptideIdentificationList load	(	const std::string &	pin_file,
		bool	higher_score_better,
		const std::string &	score_name,
		const StringList &	extra_scores,
		StringList &	filenames,
		std::string	decoy_prefix = `""`,
		double	threshold = `0.01`,
		bool	SageAnnotation = `false`
	)

static

Loads peptide identifications from a Percolator input file.

This function reads a Percolator input file (pin_file) and returns a vector of PeptideIdentification objects. It extracts relevantinformation such as peptide sequences, scores, charges, annotations, and protein accessions, applying specified thresholds and handling decoy targets as needed. Note: If a filename column is encountered the set of filenames is filled in the order of appearance and PeptideIdentifications annotated with the id_merge_index meta value to link them to the filename (similar to a merged idXML file).

Parameters

[in]	pin_file	he path to the Percolator input file with a `.pin` extension.
[in]	higher_score_better	A boolean flag indicating whether higher scores are considered better (`true`) or lower scores are better (`false`).
[in]	score_name	The name of the primary score to be used for ranking peptide hits.
[out]	extra_scores	A list of additional score names that should be extracted and stored in each `PeptideHit`.
[out]	filenames	Will be populated with the unique raw file names extracted from the input data.
[in]	decoy_prefix	The prefix used to identify decoy protein accessions. Proteins with accessions starting with this prefix are marked as decoys. Otherwise, it assumes that the pin file already contains the correctly annotated decoy status.
[in]	threshold	A double value representing the threshold for the `spectrum_q` value. Only spectra with `spectrum_q` below this threshold are processed. Implemented to allow prefiltering of Sage results.
[in]	SageAnnotation	A boolean value used to determine if the pin file is coming from Sage or not

Returns: A std::vector of PeptideIdentification objects containing the peptide identifications.

Exceptions

`Exception::ParseError` if any line in the input file does not have the expected number of columns. TODO: implement something similar to PepXMLFile().setPreferredFixedModifications(getModifications_(fixed_modifications_names));

◆ preparePin_()

static TextFile preparePin_	(	const PeptideIdentificationList &	peptide_ids,
		const StringList &	feature_set,
		const std::string &	enz,
		int	min_charge,
		int	max_charge
	)

staticprotected

◆ stampPinFeaturesOnHits() [1/2]

static std::set< std::pair< size_t, size_t > > stampPinFeaturesOnHits	(	PeptideIdentificationList &	peptide_ids,
		const std::string &	enz,
		int	min_charge,
		int	max_charge
	)

static

Compute and stamp PIN-equivalent meta values on every PeptideHit.

Runs the same per-hit computation that preparePin_ applies when writing a .pin file — but mutates the PeptideIdentifications in place instead of writing to a text file. After this call, each kept hit carries the full set of PIN meta values: SpecId, ScanNr, Label, CalcMass, ExpMass, deltamass, retentiontime, mass, score, peplen, charge1..chargeN, enzN, enzC, enzInt, dm, absdm, Peptide, Proteins.

Useful for in-process Percolator training (see OpenMS::Percolator): callers can then train on the exact same feature vectors the subprocess path would have seen via the .pin round-trip.

Hits with empty PeptideEvidences or UNKNOWN target/decoy status are left untouched; their (pid_index, hit_index) pairs are returned so callers know to skip them.

Parameters

peptide_ids	Mutated in place; each kept hit gets new meta values.
enz	Enzyme name (same values accepted as for store).
min_charge	Lower bound for the charge{N} one-hot features.
max_charge	Upper bound for the charge{N} one-hot features.

Returns: Indices of skipped hits as (pid_index, hit_index) pairs.

◆ stampPinFeaturesOnHits() [2/2]

static std::set< std::pair< size_t, size_t > > stampPinFeaturesOnHits	(	PeptideIdentificationList &	peptide_ids,
		const std::string &	enz,
		int	min_charge,
		int	max_charge,
		PinFeatureMetaValueMap &	added_meta_values
	)

static

Compute and stamp PIN-equivalent meta values, recording newly added keys.

This overload additionally records, for every kept hit, the meta-value keys that did not exist before stamping. Callers that temporarily stamp hits can use this record to remove only adapter-generated values afterwards while preserving input metadata with the same names.

Parameters

[in,out]	peptide_ids	Mutated in place; each kept hit gets PIN meta values.
[in]	enz	Enzyme name (same values accepted as for store).
[in]	min_charge	Lower bound for the charge{N} one-hot features.
[in]	max_charge	Upper bound for the charge{N} one-hot features.
[out]	added_meta_values	Newly added keys per (peptide ID, hit) index.

Returns: Indices of skipped hits as (pid_index, hit_index) pairs.

◆ store()

static void store	(	const std::string &	pin_file,
		const PeptideIdentificationList &	peptide_ids,
		const StringList &	feature_set,
		const std::string &	enz,
		int	min_charge,
		int	max_charge
	)

static

Public Types

Static Public Member Functions

Static Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ PinFeatureMetaValueMap

Member Function Documentation

◆ countEnzymatic_()

◆ getFeatureValue()

◆ getScanIdentifier()

◆ getStandardFeatureSet()

◆ isEnz_()

◆ load()

◆ preparePin_()

◆ stampPinFeaturesOnHits() [1/2]

◆ stampPinFeaturesOnHits() [2/2]

◆ store()