This class serves for reading in and writing OpenSWATH OSW files. More...

#include <OpenMS/FORMAT/OSWFile.h>

Public Member Functions
	OSWFile ()
	Default constructor. More...

virtual	~OSWFile ()
	Destructor. More...

void	read (const std::string &in_osw, const std::string &osw_level, std::stringstream &pin_output, const double &ipf_max_peakgroup_pep, const double &ipf_max_transition_isotope_overlap, const double &ipf_min_transition_sn)
	Reads an OSW SQLite file and returns the data on MS1-, MS2- or transition-level as stringstream TXT input for PercolatorAdapter. More...

void	write (const std::string &in_osw, const std::string &osw_level, const std::map< std::string, std::vector< double > > &features)
	Updates an OpenSWATH OSW SQLite files with the MS1-, MS2- or transition-level results of Percolator. More...

Detailed Description

This class serves for reading in and writing OpenSWATH OSW files.

The reader and writer returns data in a format suitable for PercolatorAdapter. OSW files have a flexible data structure. They contain all peptide query parameters of TraML/PQP files with the detected and quantified features of OpenSwathWorkflow (feature, feature_ms1, feature_ms2 & feature_transition).

The OSWFile reader extracts the feature information from the OSW file for each level (MS1, MS2 & transition) separately and generates Percolator input files. For each of the three Percolator reports, OSWFile writer adds a table (score_ms1, score_ms2, score_transition) with the respective confidence metrics. These tables can be mapped to the corresponding feature tables, are very similar to PyProphet results and can thus be used interchangeably.

Constructor & Destructor Documentation

◆ OSWFile()

OSWFile ( )

Default constructor.

◆ ~OSWFile()

virtual ~OSWFile ( )

virtual

Destructor.

Member Function Documentation

◆ read()

void read	(	const std::string &	in_osw,
		const std::string &	osw_level,
		std::stringstream &	pin_output,
		const double &	ipf_max_peakgroup_pep,
		const double &	ipf_max_transition_isotope_overlap,
		const double &	ipf_min_transition_sn
	)

Reads an OSW SQLite file and returns the data on MS1-, MS2- or transition-level as stringstream TXT input for PercolatorAdapter.

◆ write()

void write	(	const std::string &	in_osw,
		const std::string &	osw_level,
		const std::map< std::string, std::vector< double > > &	features
	)

Updates an OpenSWATH OSW SQLite files with the MS1-, MS2- or transition-level results of Percolator.