| OpenMS 2.5.0

Public Member Functions | List of all members
OSWFile Class Reference

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.