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_features	mass features to be written
precursor_peak_groups	precursor peak groups of MSn spectra that are used only when topfd_feature_out is set
scan_rt_map	scan number to retention time map
avg	averagine to determine isotope pattern range
fs	file 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_features	mass features to be written
precursor_peak_groups	precursor peak groups of MSn spectra that are used only when topfd_feature_out is set
scan_rt_map	scan number to retention time map
file_name	input spectrum file name
fs	file stream

Referenced by TOPPFLASHDeconv::main_().