Shared spectral-library preparation helper for OpenSWATH-family workflows. More...

#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathLibraryPreparation.h>

Classes
struct	AssayGeneratorParameters

struct	DecoyGeneratorParameters

struct	LibraryStats

struct	PredictedLibraryParameters

Public Member Functions
	OpenSwathLibraryPreparation ()

void	setLogType (ProgressLogger::LogType log_type)

ProgressLogger::LogType	getLogType () const

void	ensureUnimodLoaded (const AssayGeneratorParameters &parameters) const
	Ensure the requested Unimod source is loaded before modified sequences are parsed.

LibraryStats	normalizeLibraryToPQP (const std::string &input_file, FileTypes::Type input_type, const std::string &output_pqp, const Param &reader_parameters=Param()) const
	Normalize a prepared library into internal PQP format.

LibraryStats	prepareAssays (const std::string &input_file, FileTypes::Type input_type, const std::string &output_file, FileTypes::Type output_type, const AssayGeneratorParameters &parameters, const Param &reader_parameters=Param()) const
	Run assay generation / preparation and write the requested output format.

LibraryStats	generateDecoys (const std::string &input_file, FileTypes::Type input_type, const std::string &output_file, FileTypes::Type output_type, const DecoyGeneratorParameters &parameters, const Param &reader_parameters=Param()) const
	Run decoy generation and write the requested output format.

LibraryStats	prepareEmpiricalLibraryToPQP (const std::string &input_file, FileTypes::Type input_type, const std::string &output_pqp, const AssayGeneratorParameters &assay_parameters, const DecoyGeneratorParameters &decoy_parameters, const Param &reader_parameters=Param(), const std::string &scratch_directory="") const
	Prepare an empirical library by running assay generation and decoy generation into a final PQP.

LibraryStats	preparePredictedLibraryToPQP (const std::string &input_fasta, const std::string &output_pqp, const AssayGeneratorParameters &assay_parameters, const DecoyGeneratorParameters &decoy_parameters, const PredictedLibraryParameters &prediction_parameters, const std::string &scratch_directory="") const
	Build a prepared target/decoy PQP directly from FASTA using native PeptDeep prediction.

Private Attributes
ProgressLogger::LogType	log_type_ = ProgressLogger::CMD

Detailed Description

Shared spectral-library preparation helper for OpenSWATH-family workflows.

This helper centralizes the file-format-aware spectral library preparation steps that historically lived directly inside TOPP front-ends:

prepared-library normalization to PQP
assay generation / preparation
decoy generation
empirical-library preparation for full DIA workflows

The implementation mirrors the existing TOPP behavior, including the lightweight TSV/PQP/OSWPQ path where possible and the heavy TraML path when required.

Class Documentation

◆ OpenMS::OpenSwathLibraryPreparation::AssayGeneratorParameters

struct OpenMS::OpenSwathLibraryPreparation::AssayGeneratorParameters

Class Members
vector< size_t >	allowed_fragment_charges {1, 2, 3, 4}
vector< string >	allowed_fragment_types {"b", "y"}
bool	disable_decoy_transitions = false
bool	enable_detection_specific_losses = false
bool	enable_detection_unspecific_losses = false
bool	enable_identification_ms2_precursors = true
bool	enable_identification_specific_losses = true
bool	enable_identification_unspecific_losses = false
bool	enable_ipf = false
bool	enable_swath_specifity = false
int	ipf_decoy_seed = 1
size_t	max_num_alternative_localizations = 10000
Int	max_transitions = 6
Int	min_transitions = 6
double	precursor_lower_mz_limit = 400.0
double	precursor_mz_threshold = 0.025
double	precursor_upper_mz_limit = 1200.0
double	product_lower_mz_limit = 350.0
double	product_mz_threshold = 0.025
double	product_upper_mz_limit = 2000.0
bool	reuse_existing_modifications_db = false
vector< pair< double, double > >	swathes
bool	test_mode = false
string	unimod_file

◆ OpenMS::OpenSwathLibraryPreparation::DecoyGeneratorParameters

struct OpenMS::OpenSwathLibraryPreparation::DecoyGeneratorParameters

Class Members
double	aim_decoy_fraction = 1.0
vector< size_t >	allowed_fragment_charges {1, 2, 3, 4}
vector< string >	allowed_fragment_types {"b", "y"}
string	decoy_tag = "DECOY_"
bool	enable_detection_specific_losses = false
bool	enable_detection_unspecific_losses = false
string	method = "shuffle"
double	min_decoy_fraction = 0.8
double	product_mz_threshold = 0.025
bool	separate = false
double	shift_precursor_mz_shift = 0.0
double	shift_product_mz_shift = 20.0
Int	shuffle_max_attempts = 30
Int	shuffle_seed = 1	Shuffle RNG seed: 1 gives reproducible decoys, -1 uses the current time.
double	shuffle_sequence_identity_threshold = 0.5
bool	switch_kr = true

◆ OpenMS::OpenSwathLibraryPreparation::PredictedLibraryParameters

struct OpenMS::OpenSwathLibraryPreparation::PredictedLibraryParameters

Class Members
string	ccs_model_path
bool	clip_nterm_methionine {}
string	enzyme
vector< string >	fixed_modifications
Int	inference_threads {}
Int	instrument_index {}
Size	max_peptide_length {}
Size	max_variable_modifications {}
Size	min_peptide_length {}
Size	missed_cleavages {}
string	ms2_model_path
double	nce {}
vector< Int >	precursor_charges
bool	predict_ccs {}
Size	prediction_batch_size {}
string	rt_model_path
vector< string >	variable_modifications

Constructor & Destructor Documentation

◆ OpenSwathLibraryPreparation()

OpenSwathLibraryPreparation ( )

Member Function Documentation

◆ ensureUnimodLoaded()

void ensureUnimodLoaded ( const AssayGeneratorParameters & parameters ) const

Ensure the requested Unimod source is loaded before modified sequences are parsed.

◆ generateDecoys()

LibraryStats generateDecoys	(	const std::string &	input_file,
		FileTypes::Type	input_type,
		const std::string &	output_file,
		FileTypes::Type	output_type,
		const DecoyGeneratorParameters &	parameters,
		const Param &	reader_parameters = `Param()`
	)		const

Run decoy generation and write the requested output format.

◆ getLogType()

ProgressLogger::LogType getLogType ( ) const

◆ normalizeLibraryToPQP()

LibraryStats normalizeLibraryToPQP	(	const std::string &	input_file,
		FileTypes::Type	input_type,
		const std::string &	output_pqp,
		const Param &	reader_parameters = `Param()`
	)		const

Normalize a prepared library into internal PQP format.

◆ prepareAssays()

LibraryStats prepareAssays	(	const std::string &	input_file,
		FileTypes::Type	input_type,
		const std::string &	output_file,
		FileTypes::Type	output_type,
		const AssayGeneratorParameters &	parameters,
		const Param &	reader_parameters = `Param()`
	)		const

Run assay generation / preparation and write the requested output format.

◆ prepareEmpiricalLibraryToPQP()

LibraryStats prepareEmpiricalLibraryToPQP	(	const std::string &	input_file,
		FileTypes::Type	input_type,
		const std::string &	output_pqp,
		const AssayGeneratorParameters &	assay_parameters,
		const DecoyGeneratorParameters &	decoy_parameters,
		const Param &	reader_parameters = `Param()`,
		const std::string &	scratch_directory = `""`
	)		const

Prepare an empirical library by running assay generation and decoy generation into a final PQP.

Parameters

input_file	Input transition library file.
input_type	File type of the input transition library.
output_pqp	Output path for the prepared target/decoy PQP library.
assay_parameters	Assay-generation parameters applied before decoy generation.
decoy_parameters	Decoy-generation parameters used for the prepared assays.
reader_parameters	Optional parameters passed to the transition-library reader.
scratch_directory	Optional directory for the temporary assay-preparation file. The intermediate gets a unique per-invocation file name, so concurrent callers can share this directory without sharing or overwriting the same intermediate. No subdirectory is created, which keeps paths short on Windows. The file is removed on both success and failure. When empty, a fresh system temporary directory is used.

◆ preparePredictedLibraryToPQP()

LibraryStats preparePredictedLibraryToPQP	(	const std::string &	input_fasta,
		const std::string &	output_pqp,
		const AssayGeneratorParameters &	assay_parameters,
		const DecoyGeneratorParameters &	decoy_parameters,
		const PredictedLibraryParameters &	prediction_parameters,
		const std::string &	scratch_directory = `""`
	)		const

Build a prepared target/decoy PQP directly from FASTA using native PeptDeep prediction.

FASTA entries whose identifier starts with decoy_parameters.decoy_tag, or carries a decoy affix detected by DecoyHelper::findDecoyString, are skipped.

Prediction batches are spilled to disk; global UIS/decoy generation still materializes the library.

Parameters

[in]	input_fasta	FASTA file to digest and predict.
[in]	output_pqp	Prepared target/decoy library.
[in]	assay_parameters	Assay filtering and UIS settings.
[in]	decoy_parameters	Decoy generation settings.
[in]	prediction_parameters	Digestion and prediction settings (charges must be unique).
[in]	scratch_directory	Directory for temporary prediction batches; empty uses the system temporary directory. Scratch files are removed on success and failure.

The method remains available in non-ONNX builds but throws Exception::Precondition when called.

◆ setLogType()

void setLogType ( ProgressLogger::LogType log_type )

Member Data Documentation

◆ log_type_

ProgressLogger::LogType log_type_ = ProgressLogger::CMD

private

Classes

Public Member Functions

Private Attributes