OSWFile Class Reference

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

#include <OpenMS/FORMAT/OSWFile.h>

Collaboration diagram for OSWFile:

Classes
struct	PercolatorFeature

Public Types
enum	OSWLevel { MS1, MS2, TRANSITION, SIZE_OF_OSWLEVEL }

Static Public Member Functions
static void	readToPIN (const std::string &in_osw, const OSWFile::OSWLevel osw_level, std::ostream &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 ostream (e.g. stringstream or ofstream). More...
static void	writeFromPercolator (const std::string &in_osw, const OSWFile::OSWLevel osw_level, const std::map< std::string, PercolatorFeature > &features)
	Updates an OpenSWATH OSW SQLite files with the MS1-, MS2- or transition-level results of Percolator. More...

Static Public Attributes
static const std::array< std::string,(Size) OSWLevel::SIZE_OF_OSWLEVEL >	names_of_oswlevel

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.

Member Enumeration Documentation

OSWLevel

enum OSWLevel

strong

Enumerator
MS1
MS2
TRANSITION
SIZE_OF_OSWLEVEL

Member Function Documentation

readToPIN()

static void readToPIN ( const std::string &  in_osw, const OSWFile::OSWLevel  osw_level, std::ostream &  pin_output, const double  ipf_max_peakgroup_pep, const double  ipf_max_transition_isotope_overlap, const double  ipf_min_transition_sn  )

static

Reads an OSW SQLite file and returns the data on MS1-, MS2- or transition-level as ostream (e.g. stringstream or ofstream).

writeFromPercolator()

static void writeFromPercolator ( const std::string &  in_osw, const OSWFile::OSWLevel  osw_level, const std::map< std::string, PercolatorFeature > &  features  )

static

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

Member Data Documentation

names_of_oswlevel

const std::array<std::string, (Size)OSWLevel::SIZE_OF_OSWLEVEL> names_of_oswlevel

static