FLASHDeconvSpectrumFile Class Reference

FLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats. More...

#include <OpenMS/FORMAT/FLASHDeconvSpectrumFile.h>

Static Public Member Functions
static void	writeDeconvolvedMassesHeader (std::fstream &fs, uint ms_level, bool detail, bool decoy)
	write the header in the tsv output file (spectrum level) More...
static void	writeDeconvolvedMasses (DeconvolvedSpectrum &dspec, std::fstream &fs, const String &file_name, const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg, double tol, bool write_detail, bool decoy)
	write the deconvolved masses in the output file (spectrum level) More...
static void	writeTopFD (const DeconvolvedSpectrum &dspec, std::fstream &fs, double snr_threshold=1.0, double decoy_harmonic_factor=1.0, double decoy_precursor_offset=.0)
	write the deconvolved masses TopFD output (*.msalign) More...

Static Private Attributes
static const int	topFD_min_peak_count_ = 3
	number of minimum peak count in topFD msalign file More...
static const int	topFD_max_peak_count_ = 500
	number of maximum peak count in topFD msalign file More...

Detailed Description

FLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats.

Member Function Documentation

writeDeconvolvedMasses()

static void writeDeconvolvedMasses ( DeconvolvedSpectrum &  dspec, std::fstream &  fs, const String &  file_name, const FLASHDeconvHelperStructs::PrecalculatedAveragine &  avg, double  tol, bool  write_detail, bool  decoy  )

static

write the deconvolved masses in the output file (spectrum level)

Parameters

dspec	deconvolved spectrum to write
fs	file stream to the output file
file_name	the output file name that the deconvolved masses will be written.
avg	averagine information to calculate monoisotopic and average mass difference within this function. In PeakGroup (peaks of DeconvolvedSpectrum) only monoisotopic mass is recorded. To write both monoisotopic and average masses, their mass difference should be calculated using this averagine information.
tol	mass tolerance
write_detail	if this is set, more detailed information on each mass will be written in the output file.
decoy	if set true, decoy and qvalue information will be written. Default MS1 headers are: FileName, ScanNum, Decoy, RetentionTime, MassCountInSpec, AverageMass, MonoisotopicMass, SumIntensity, MinCharge, MaxCharge, PeakCount, IsotopeCosine, ChargeScore, MassSNR, ChargeSNR, RepresentativeCharge, RepresentativeMzStart, RepresentativeMzEnd, QScore, PerChargeIntensity, PerIsotopeIntensity

Default MS2 headers include MS1 headers plus: PrecursorScanNum, PrecursorMz, PrecursorIntensity, PrecursorCharge, PrecursorSNR, PrecursorMonoisotopicMass, PrecursorQScore

Detailed MS1 and MS2 headers include all corresponding headers above plus: PeakMZs, PeakIntensities, PeakCharges, PeakMasses, PeakIsotopeIndices, PeakPPMErrors

Referenced by TOPPFLASHDeconv::main_().

writeDeconvolvedMassesHeader()

static void writeDeconvolvedMassesHeader ( std::fstream &  fs, uint  ms_level, bool  detail, bool  decoy  )

static

write the header in the tsv output file (spectrum level)

Parameters

fs	file stream to the output file
ms_level	ms level of the spectrum
detail	if set true, detailed information of the mass (e.g., peak list for the mass) is written
decoy	if set true, decoy and qvalue information will be written.

Referenced by TOPPFLASHDeconv::main_().

writeTopFD()

static void writeTopFD ( const DeconvolvedSpectrum &  dspec, std::fstream &  fs, double  snr_threshold = 1.0, double  decoy_harmonic_factor = 1.0, double  decoy_precursor_offset = .0  )

static

write the deconvolved masses TopFD output (*.msalign)

Parameters

dspec	deconvolved spectrum to write
fs	file stream to the output file
snr_threshold	SNR threshold to filter out low SNR precursors. Even if a PeakGroup has a high deconvolution quality, it should be still discarded for identification when its precursor SNR (SNR within the isolation window) is too low.
decoy_harmonic_factor	this factor will be multiplied to precursor mass and charge. To generate decoy spectra
decoy_precursor_offset	this value will be added to precursor mass. To generate decoy spectra

Referenced by TOPPFLASHDeconv::main_().

Member Data Documentation

topFD_max_peak_count_

const int topFD_max_peak_count_ = 500

staticprivate

number of maximum peak count in topFD msalign file

topFD_min_peak_count_

const int topFD_min_peak_count_ = 3

staticprivate

number of minimum peak count in topFD msalign file