OpenMS
FLASHDeconvFeatureFile Class Reference

FLASHDeconv feature level output *.tsv, *.ms1ft (for Promex), *.feature (for TopPIC) file formats. More...

#include <OpenMS/FORMAT/FLASHDeconvFeatureFile.h>

Static Public Member Functions

static void writeHeader (std::fstream &fs)
 write header line for regular file output More...
 
static void writePromexHeader (std::fstream &fs)
 write header line for promex file output More...
 
static void writeTopFDFeatureHeader (std::vector< std::fstream > &fs)
 write header line for topFD feature files More...
 
static void writeFeatures (const std::vector< FLASHDeconvHelperStructs::MassFeature > &mass_features, const String &file_name, std::fstream &fs)
 write the features in regular file output More...
 
static void writeTopFDFeatures (const std::vector< FLASHDeconvHelperStructs::MassFeature > &mass_features, const std::map< int, PeakGroup > &precursor_peak_groups, const std::map< int, double > &scan_rt_map, const String &file_name, std::vector< std::fstream > &fs)
 Find mass features and write features in TopFD format files. More...
 
static void writePromexFeatures (const std::vector< FLASHDeconvHelperStructs::MassFeature > &mass_features, const std::map< int, PeakGroup > &precursor_peak_groups, const std::map< int, double > &scan_rt_map, const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg, std::fstream &fs)
 Find mass features and write features in Promex format files. More...
 

Detailed Description

FLASHDeconv feature level output *.tsv, *.ms1ft (for Promex), *.feature (for TopPIC) file formats.

Member Function Documentation

◆ writeFeatures()

static void writeFeatures ( const std::vector< FLASHDeconvHelperStructs::MassFeature > &  mass_features,
const String file_name,
std::fstream &  fs 
)
static

write the features in regular file output

Referenced by TOPPFLASHDeconv::main_().

◆ writeHeader()

static void writeHeader ( std::fstream &  fs)
static

write header line for regular file output

Referenced by TOPPFLASHDeconv::main_().

◆ writePromexFeatures()

static void writePromexFeatures ( const std::vector< FLASHDeconvHelperStructs::MassFeature > &  mass_features,
const std::map< int, PeakGroup > &  precursor_peak_groups,
const std::map< int, double > &  scan_rt_map,
const FLASHDeconvHelperStructs::PrecalculatedAveragine avg,
std::fstream &  fs 
)
static

Find mass features and write features in Promex format files.

Parameters
mass_featuresmass features to be written
precursor_peak_groupsprecursor peak groups of MSn spectra that are used only when topfd_feature_out is set
scan_rt_mapscan number to retention time map
avgaveragine to determine isotope pattern range
fsfile stream

Referenced by TOPPFLASHDeconv::main_().

◆ writePromexHeader()

static void writePromexHeader ( std::fstream &  fs)
static

write header line for promex file output

Referenced by TOPPFLASHDeconv::main_().

◆ writeTopFDFeatureHeader()

static void writeTopFDFeatureHeader ( std::vector< std::fstream > &  fs)
static

write header line for topFD feature files

Referenced by TOPPFLASHDeconv::main_().

◆ writeTopFDFeatures()

static void writeTopFDFeatures ( const std::vector< FLASHDeconvHelperStructs::MassFeature > &  mass_features,
const std::map< int, PeakGroup > &  precursor_peak_groups,
const std::map< int, double > &  scan_rt_map,
const String file_name,
std::vector< std::fstream > &  fs 
)
static

Find mass features and write features in TopFD format files.

Parameters
mass_featuresmass features to be written
precursor_peak_groupsprecursor peak groups of MSn spectra that are used only when topfd_feature_out is set
scan_rt_mapscan number to retention time map
file_nameinput spectrum file name
fsfile stream

Referenced by TOPPFLASHDeconv::main_().